From 2447a74a5ea9e32c4247ceb7f2897efd7881eeb7 Mon Sep 17 00:00:00 2001 From: azadsadr Date: Tue, 17 Sep 2024 15:42:09 +0000 Subject: [PATCH] Built site for bascule@0.1.0: ca0ae76 --- articles/Fit_breast_data.html | 64 +++++++++++------- ...ed-chunk-7-2.png => unnamed-chunk-8-1.png} | Bin ...ed-chunk-7-3.png => unnamed-chunk-9-1.png} | Bin pkgdown.yml | 2 +- search.json | 2 +- 5 files changed, 41 insertions(+), 27 deletions(-) rename articles/Fit_breast_data_files/figure-html/{unnamed-chunk-7-2.png => unnamed-chunk-8-1.png} (100%) rename articles/Fit_breast_data_files/figure-html/{unnamed-chunk-7-3.png => unnamed-chunk-9-1.png} (100%) diff --git a/articles/Fit_breast_data.html b/articles/Fit_breast_data.html index 4ee5d60..bf554d9 100644 --- a/articles/Fit_breast_data.html +++ b/articles/Fit_breast_data.html @@ -64,6 +64,9 @@ +
+

Package Setup +

 library(bascule)
 #> ✔ Loading bascule. Support : <https://caravagnalab.github.io/bascule/>
@@ -71,16 +74,22 @@ knitr::opts_chunk$set(warning = FALSE, message = FALSE) configure_environment(envname="bascule-env", use_default=TRUE) py = reticulate::import("pybascule")
+
-

Fit the model +

Model Fitting

+

Here, we load the breast tumor type fit object +(breast_data) from the bascule package, and retrieve the +input data (counts) from the loaded fit object.

 data("breast_data")
-x = breast_data$x
+x = breast_data$x +counts = get_input(x, matrix=TRUE, reconstructed=FALSE)
+

We execute the fit function using the input data +(counts).

-counts = get_input(breast_data$x, matrix=TRUE, reconstructed=FALSE)
-x_pre_refinement = fit(
-  counts=breast_data$counts,
+x_pre_refinement = fit(
+  counts=counts,
   k_list=0:25,
   cluster=15,
   reference_cat=breast_data$reference_cat,
@@ -94,17 +103,18 @@ 
Fit the model)
-

Refine the signatures +

Signature Refinement

-

Here, we are trying to eliminate all de novo signatures that are +

Here, we eliminate all inferred de novo signatures that are explainable with linear combination of the other signatures.

 x_refined = refine_denovo_signatures(x_pre_refinement)
-

Re-Clustering +

Patients Re-Clustering

-

we perform the clustering step, using the new set of signatures.

+

We redo the clustering step (if applicable), using the new set of the +signatures and updated exposure matrix.

 x = fit_clustering(
   x_pre_refinement,
@@ -119,33 +129,37 @@ 
Re-Clusteringx = x %>% merge_clusters()
-

Visualization +

Output Visualization +

+
+
+

Mutational Signatures Visualization 

-plot_signatures(x)
-#> Warning: This manual palette can handle a maximum of 16 values. You have
-#> supplied 18
+plot_signatures(x)

+
+

Exposure Matrix Visualization +

-
-plot_exposures(x)
+plot_exposures(x)
 #> Scale for fill is already present.
 #> Adding another scale for fill, which will replace the existing scale.
 #> Scale for fill is already present.
 #> Adding another scale for fill, which will replace the existing scale.
 #> Scale for fill is already present.
-#> Adding another scale for fill, which will replace the existing scale.
-#> Warning: No shared levels found between `names(values)` of the manual scale and the
-#> data's colour values.
-

+#> Adding another scale for fill, which will replace the existing scale.
+

+ +
+

Clusters Centroids Visualization +

-
-plot_centroids(x)
+plot_centroids(x)
 #> Scale for fill is already present.
-#> Adding another scale for fill, which will replace the existing scale.
-#> Warning: No shared levels found between `names(values)` of the manual scale and the
-#> data's colour values.
-

+#> Adding another scale for fill, which will replace the existing scale.
+

+ diff --git a/articles/Fit_breast_data_files/figure-html/unnamed-chunk-7-2.png b/articles/Fit_breast_data_files/figure-html/unnamed-chunk-8-1.png similarity index 100% rename from articles/Fit_breast_data_files/figure-html/unnamed-chunk-7-2.png rename to articles/Fit_breast_data_files/figure-html/unnamed-chunk-8-1.png diff --git a/articles/Fit_breast_data_files/figure-html/unnamed-chunk-7-3.png b/articles/Fit_breast_data_files/figure-html/unnamed-chunk-9-1.png similarity index 100% rename from articles/Fit_breast_data_files/figure-html/unnamed-chunk-7-3.png rename to articles/Fit_breast_data_files/figure-html/unnamed-chunk-9-1.png diff --git a/pkgdown.yml b/pkgdown.yml index 2f1f479..47d2696 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,7 +5,7 @@ articles: bascule: bascule.html articles/Fit_breast_data: Fit_breast_data.html articles/Inference: Inference.html -last_built: 2024-09-17T13:59Z +last_built: 2024-09-17T15:41Z urls: reference: https:://caravagnalab.github.io/bascule/reference article: https:://caravagnalab.github.io/bascule/articles diff --git a/search.json b/search.json index 5d14c5b..0af7e76 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"fit-the-model","dir":"Articles","previous_headings":"","what":"Fit the model","title":"Fit on real data","text":"","code":"data(\"breast_data\") x = breast_data$x counts = get_input(breast_data$x, matrix=TRUE, reconstructed=FALSE) x_pre_refinement = fit( counts=breast_data$counts, k_list=0:25, cluster=15, reference_cat=breast_data$reference_cat, n_steps=3000, lr=0.005, seed_list=c(19,255,18321,331), hyperparameters=list(\"penalty_scale\"=0, \"alpha_conc\"=alpha_conc), store_fits=TRUE, py=py, CUDA=TRUE, autoguide=TRUE )"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"refine-the-signatures","dir":"Articles","previous_headings":"","what":"Refine the signatures","title":"Fit on real data","text":", trying eliminate de novo signatures explainable linear combination signatures.","code":"x_refined = refine_denovo_signatures(x_pre_refinement)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"re-clustering","dir":"Articles","previous_headings":"","what":"Re-Clustering","title":"Fit on real data","text":"perform clustering step, using new set signatures.","code":"x = fit_clustering( x_pre_refinement, cluster=15, seed_list=c(19,255,18321,331), hyperparameters=list(\"penalty_scale\"=0, \"alpha_conc\"=alpha_conc), store_fits=TRUE, py=py, CUDA=TRUE, autoguide=TRUE ) x = x %>% merge_clusters()"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"visualization","dir":"Articles","previous_headings":"","what":"Visualization","title":"Fit on real data","text":"","code":"plot_signatures(x) #> Warning: This manual palette can handle a maximum of 16 values. You have #> supplied 18 plot_exposures(x) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values. plot_centroids(x) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values."},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"load-datasets","dir":"Articles","previous_headings":"","what":"Load datasets","title":"Inference","text":"can load data example_dataset, bascule object containing true signatures exposures used generate mutation counts matrix. object, data SBS DBS reported. can extract mutation count matrix object using get_input function. reconstructed=FALSE obtaining observed counts, reconstructed ones computed matrix multiplication exposures signatures. use reference COSMIC catalogue SBS DBS. example dataset, true number signatures five SBS DBS, thus can provide list K test values 0 7.","code":"data(\"synthetic_data\") counts = synthetic_data$counts head(counts[[\"SBS\"]][, 1:10]) #> A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T A[C>T]A #> G1_1 118 7 0 52 10 2 1 5 27 #> G1_2 236 21 5 107 17 12 3 14 67 #> G1_3 132 8 1 50 11 5 1 7 42 #> G1_4 116 15 3 40 10 6 0 12 40 #> G1_5 149 12 3 56 10 3 2 14 49 #> G1_6 161 10 2 66 13 8 4 13 62 #> A[C>T]C #> G1_1 10 #> G1_2 35 #> G1_3 19 #> G1_4 26 #> G1_5 16 #> G1_6 25 head(counts[[\"DBS\"]][, 1:10]) #> AC>CA AC>CG AC>CT AC>GA AC>GG AC>GT AC>TA AC>TG AC>TT AT>CA #> G1_1 5 1 4 8 4 12 5 0 6 13 #> G1_2 4 1 6 4 3 17 0 1 3 16 #> G1_3 5 0 4 6 1 13 1 0 2 18 #> G1_4 2 0 0 2 0 4 1 1 2 3 #> G1_5 4 0 4 3 0 6 0 1 2 8 #> G1_6 0 0 3 1 0 5 0 1 1 1 reference_cat = list(\"SBS\"=COSMIC_sbs_filt, \"DBS\"=COSMIC_dbs) K_list = 0:7"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"fit-the-model","dir":"Articles","previous_headings":"","what":"Fit the model","title":"Inference","text":"Now, can fit model. Let’s first fit NMF perform signatures deconvolution.","code":"x = fit(counts=counts, k_list=K_list, n_steps=3000, reference_cat=reference_cat, keep_sigs=c(\"SBS1\",\"SBS5\"), # force fixed signatures store_fits=TRUE, py=py) x = synthetic_data$x"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualize-the-inference-scores","dir":"Articles","previous_headings":"","what":"Visualize the inference scores","title":"Inference","text":"can inspect model selection procedure.","code":"plot_scores(x) #> Joining with `by = join_by(parname, value_fit, seed, type)` plot_gradient_norms(x)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualize-the-inferred-parameters","dir":"Articles","previous_headings":"","what":"Visualize the inferred parameters","title":"Inference","text":"can visualize inferred signatures. , notice 41 20 SBS DBS signatures, model selects 6 5 signatures catalogue. Moreover, also infers denovo signature SBS counts.","code":"plot_signatures(x)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"post-fit-heuristics-and-clustering","dir":"Articles","previous_headings":"","what":"Post fit heuristics and clustering","title":"Inference","text":"can notice signatures plots clear similarity certain signatures. can compute linear combination de novo signatures remove similar reference ones. refined set signatures can run model perform clustering samples based exposures.","code":"x_refined = refine_denovo_signatures(x) x_refined_cluster = fit_clustering(x_refined, cluster=3) x_refined_cluster = synthetic_data$x_refined_cluster"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualise-clustering-results","dir":"Articles","previous_headings":"","what":"Visualise clustering results","title":"Inference","text":"","code":"plot_signatures(x_refined_cluster) plot_centroids(x_refined_cluster) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values. plot_exposures(x_refined_cluster) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values."},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"installation-of-the-package","dir":"Articles","previous_headings":"","what":"Installation of the package","title":"bascule","text":"can install bascule GitHub using devtools. Load package.","code":"devtools::install_github(\"caravagnalab/bascule\") library(bascule)"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"python-dependencies-installation","dir":"Articles","previous_headings":"","what":"Python dependencies installation","title":"bascule","text":"package loaded, might execute configure_environment() function automatically check whether: version Anaconda Miniconda available, otherwise Miniconda installation started, conda environment loaded, package check bascule-env present, otherwise created, use existing conda environment, can loaded loading package, either reticulate function reticulate::use_condaenv() using bascule function load_conda_env(): eventually, required Python dependencies installed loaded environment, installed.","code":"reticulate::use_condaenv(\"env-name\", required=TRUE) load_conda_env(envname=\"env-name\")"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"functions-to-manually-configure-an-environment","dir":"Articles","previous_headings":"","what":"Functions to manually configure an environment","title":"bascule","text":"function configure_environment() can used interactively manually configure existing environment, create one scratch. function first check Anaconda Miniconda installation available, otherwise prompt Miniconda installation. input name environment either name existing environment name environment created. environment loaded created, required Python dependencies installed.","code":"configure_environment(env_name=\"bascule-env\", use_default=F)"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"check-the-loaded-python-version-and-environment","dir":"Articles","previous_headings":"","what":"Check the loaded Python version and environment","title":"bascule","text":"package provides also set helper functions check environment loaded. have_loaded_env() check environment already loaded, which_conda_env() check environment loaded. have_python_deps() check Python packages list installed specified environment. load_conda_env() load specified environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Elena Buscaroli. Author, maintainer. Azad Sadr. Author, maintainer. Giulio Caravagna. Author.","code":""},{"path":"https:://caravagnalab.github.io/bascule/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Buscaroli E, Sadr , Caravagna G (2024). bascule: bascule. R package version 0.1.0, https://caravagnalab.github.io/bascule/, https://github.com/caravagnalab/bascule.","code":"@Manual{, title = {bascule: bascule}, author = {Elena Buscaroli and Azad Sadr and Giulio Caravagna}, year = {2024}, note = {R package version 0.1.0, https://caravagnalab.github.io/bascule/}, url = {https://github.com/caravagnalab/bascule}, }"},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"bascule-","dir":"","previous_headings":"","what":"bascule","title":"bascule","text":"Bascule Bayesian model fit multiple signature types multiple patients, leveraging pre-existing catalogue known signatures COSMIC. Bascule searches known signatures input catalogue well new signatures outside catalogue, accounting hidden structure input data (e.g., distinct tumour types). Moreover, bascule performs tensor clustering retrieve latent groups input cohort exposures multiple signature types jointly. model uses non-negative matrix factorisation variational inference implemented pybascule Python package.","code":""},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"bascule","text":"use bascule, please cite: ……","code":""},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"bascule","text":"can install released version bascule GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"caravagnalab/bascule\")"},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"copyright-and-contacts","dir":"","previous_headings":"Installation","what":"Copyright and contacts","title":"bascule","text":"Elena Buscaroli, Azad Sadr, Giulio Caravagna. Cancer Data Science (CDS) Laboratory, University Trieste, Italy.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"COSMIC catalogue CN (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"","code":"data(COSMIC_cn)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"object class data.frame 24 rows 48 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"COSMIC catalogue DBS (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"","code":"data(COSMIC_dbs)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"object class data.frame 20 rows 78 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"COSMIC catalogue Indels (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"","code":"data(COSMIC_indels)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"object class data.frame 18 rows 83 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"COSMIC catalogue SBS (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"","code":"data(COSMIC_sbs)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"Filtered version COSMIC catalogue. validated signatures present. signature (besides SBS5) contexts probability mass 0.02 set 0 probabilities re-normalized contexts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"","code":"data(COSMIC_sbs_filt)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":null,"dir":"Reference","previous_headings":"","what":"Degasperi DBS catalogue — Degasperi_DBS","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"DBS signatures extracted released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"","code":"data(Degasperi_DBS)"},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"object class data.frame 39 rows 78 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":null,"dir":"Reference","previous_headings":"","what":"Degasperi SBS catalogue — Degasperi_SBS","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"SBS signatures extracted released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"","code":"data(Degasperi_SBS)"},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"object class data.frame 120 rows 96 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/bascule-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bascule: bascule — bascule-package","title":"bascule: bascule — bascule-package","text":"packages provides bascule (Bayesian inference clustering mutational signatures established catalogue) algorithm detect single-nucleotide substituion signatures cancer. bascule provides full Bayesian formulation based non-negative matrix factorisation, leveraging catalogue known signatures. tool specifically developed detect de novo mutational signatures type (SBS, DBS, IDS, ...) different pre-defined reference catalogue perform clustering samples signature types jointly.","code":""},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/reference/bascule-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bascule: bascule — bascule-package","text":"Maintainer: Elena Buscaroli ele.buscaroli@gmail.com Authors: Giulio Caravagna gcaravagn@gmail.com","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis of breast tumours — breast_data","title":"Analysis of breast tumours — breast_data","text":"Input SBS DBS counts BASCULE fits 2682 breast tumours released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis of breast tumours — breast_data","text":"","code":"data(breast_data)"},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Analysis of breast tumours — breast_data","text":"object class list length 2.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Configure the reticulate environment — configure_environment","title":"Configure the reticulate environment — configure_environment","text":"Function configure Python dependencies R. Python environment available, function check version conda miniconda, otherwise install miniconda, install Python package pybascule.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Configure the reticulate environment — configure_environment","text":"","code":"configure_environment(envname = \"bascule-env\", use_default = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Configure the reticulate environment — configure_environment","text":"env_name name conda environment use, available.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to map de novo signatures to input catalogues — convert_dn_names","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"Function map de novo signatures input catalogues","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"","code":"convert_dn_names(x, x.simul = NULL, reference_cat = NULL, cutoff = 0.8)"},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"x Object class \"bascule_obj\" x.simul Another object class \"bascule_obj\". present, `x` de novo signatures mapped `x_simul` ones reference_cat List reference catalogues. `NULL`, `x` de novo signatures mapped catalogues. cutoff Threshold cosine similarity.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"Modified version `x` mapped de novo names renamed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a bascule object — fit","title":"Fit a bascule object — fit","text":"Fit bascule object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a bascule object — fit","text":"","code":"fit( counts, k_list, cluster = NULL, reference_cat = list(SBS = COSMIC_filt, DBS = COSMIC_dbs), keep_sigs = c(\"SBS1\", \"SBS5\"), hyperparameters = NULL, lr = 0.005, optim_gamma = 0.1, n_steps = 3000, py = NULL, enumer = \"parallel\", nonparametric = TRUE, autoguide = FALSE, filter_dn = FALSE, min_exposure = 0.2, CUDA = TRUE, compile = FALSE, store_parameters = FALSE, store_fits = TRUE, seed_list = c(10) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a bascule object — fit","text":"counts List mutation counts matrices multiple variant types. k_list List number denovo signatures test. cluster Maximum number clusters. `NULL`, clustering performed. reference_cat List reference catalogues use NMF. Names must input counts. keep_sigs List reference signatures keep even found low exposures. hyperparameters List hyperparameters passed NMF clustering models. lr Learning rate used SVI. optim_gamma Deprecated n_steps Number iterations inference. py User-installed version pybascule package enumer Enumeration used clustering (either `parallel` `sequential`). nonparametric Deprecated. model works nonparametric way. autoguide Logical. `TRUE`, clustering model use Pyro autoguide. filter_dn Logical. `TRUE`, contexts 0.01 denovo signatures set 0, provided filtered signatures remain consistent inferred ones. min_exposure Reference signatures exposures lower `min_exposure` dropped. CUDA Logical. `TRUE` GPU available, models run GPU. compile Deprecated. store_parameters Logical. `TRUE`, parameters every step inference stored object. store_fits Logical. `TRUE`, tested fits, .e., every value `K`, stored object. seed_list List seeds used every input configuration.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a bascule object — fit","text":"Bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit clustering — fit_clustering","title":"Fit clustering — fit_clustering","text":"Fit clustering","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit clustering — fit_clustering","text":"","code":"fit_clustering( x, cluster, hyperparameters = NULL, lr = 0.005, optim_gamma = 0.1, n_steps = 3000, py = NULL, enumer = \"parallel\", nonparametric = TRUE, autoguide = TRUE, CUDA = TRUE, compile = FALSE, store_parameters = FALSE, store_fits = TRUE, seed_list = c(10) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit clustering — fit_clustering","text":"x Bascule object signatures deconvolution performed. cluster Maximum number clusters. hyperparameters List hyperparameters passed NMF clustering models. lr Learning rate SVI optimizer. optim_gamma Deprecated. n_steps Number steps inference. py User-installed version pybascule package enumer Enumeration used clustering (either `parallel` `sequential`). nonparametric Deprecated. model works nonparametric way. autoguide Logical. `TRUE`, clustering model use Pyro autoguide. CUDA Logical. `TRUE` GPU available, models run GPU. compile Deprecated. store_parameters Logical. `TRUE`, parameters every step inference stored object. store_fits Logical. `TRUE`, tested fits, .e., every value `K`, stored object. seed_list List seeds used every input configuration.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit clustering — fit_clustering","text":"Bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get denovo signatures names — get_denovo_signames","title":"Get denovo signatures names — get_denovo_signames","text":"Get denovo signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get denovo signatures names — get_denovo_signames","text":"","code":"get_denovo_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get denovo signatures names — get_denovo_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get denovo signatures names — get_denovo_signames","text":"list de novo signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get de novo (reference) signatures — get_denovo_signatures","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"Get de novo (reference) signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"","code":"get_denovo_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"De novo signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"Get exposures — get_exposure","title":"Get exposures — get_exposure","text":"Get exposures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get exposures — get_exposure","text":"","code":"get_exposure( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), add_groups = FALSE, matrix = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get exposures — get_exposure","text":"x bascule object. types List variant types retrieve signames . samples List samples report exposures . clusters List cluster labels report exposures . add_groups Logical. `TRUE` add column sample's group label. matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get exposures — get_exposure","text":"Exposures matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get reference signatures names — get_fixed_signames","title":"Get reference signatures names — get_fixed_signames","text":"Get reference signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get reference signatures names — get_fixed_signames","text":"","code":"get_fixed_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get reference signatures names — get_fixed_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get reference signatures names — get_fixed_signames","text":"list reference signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get fixed (reference) signatures — get_fixed_signatures","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"Get fixed (reference) signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"","code":"get_fixed_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"Reference signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Get input data — get_input","title":"Get input data — get_input","text":"Get input data","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get input data — get_input","text":"","code":"get_input( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), matrix = FALSE, reconstructed = FALSE, add_groups = FALSE, by_sigs = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get input data — get_input","text":"x bascule object. types List variant types subset samples List samples subset clusters List clusters subset matrix Logical. `TRUE`, output wide format. reconstructed Logical. `TRUE`, reconstructed counts, .e., computed alpha x beta, returned. add_groups Logical. `TRUE` clustering performed, sample annotated assigned group. by_sigs Logical. `TRUE`, number mutations generated signature returned.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get input data — get_input","text":"list long wide-formatted mutations counts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get signatures names — get_signames","title":"Get signatures names — get_signames","text":"Get signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get signatures names — get_signames","text":"","code":"get_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get signatures names — get_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get signatures names — get_signames","text":"list signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get signatures — get_signatures","title":"Get signatures — get_signatures","text":"Get signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get signatures — get_signatures","text":"","code":"get_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get signatures — get_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get signatures — get_signatures","text":"Signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if there is a loaded conda environment. — have_loaded_env","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"Function check conda environment already loaded.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"","code":"have_loaded_env()"},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"Boolean, TRUE environment loaded, FALSE otherwise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if Python packages are installed in the environment. — have_python_deps","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"Function check one Python packages present conda environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"","code":"have_python_deps(envname = \"\", py_pkgs = c(\"pybascule\"))"},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"envname name environment check. empty, function check currently loaded environment. py_pkgs list vector Python packages.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"list Boolean. input package, TRUE package installed, FALSE otherwise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/load_conda_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Load the input conda environment. — load_conda_env","title":"Load the input conda environment. — load_conda_env","text":"Function load input conda environment. function raise error Python version already attached reticulate package. case, necessary restart R session load desired environment **** calling lineaGT function interfacing Python - filter_dataset() fit().","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/load_conda_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load the input conda environment. — load_conda_env","text":"","code":"load_conda_env(envname = \"bascule-env\")"},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to merge similar clusters — merge_clusters","title":"Function to merge similar clusters — merge_clusters","text":"function iteratively merge clusters result similar centroid. merging stop soon cosine similarity pairs clusters `cutoff`","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to merge similar clusters — merge_clusters","text":"","code":"merge_clusters(x, cutoff = 0.8)"},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to merge similar clusters — merge_clusters","text":"x bascule object. cutoff Minimum value similarity merge two clusters.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to merge similar clusters — merge_clusters","text":"bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot for class 'bascule_obj'. — plot.bascule_obj","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"default plot CNA segments wide format","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"","code":"# S3 method for class 'bascule_obj' plot(x, ...)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"x obj class 'bascule_obj'. ... Default S3 method parameter.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"Nothing.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot clustering centroids — plot_centroids","title":"Plot clustering centroids — plot_centroids","text":"Plot clustering centroids","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot clustering centroids — plot_centroids","text":"","code":"plot_centroids( x, types = get_types(x), clusters = get_cluster_labels(x), cls = NULL, sort_by = NULL, exposure_thr = 0, quantile_thr = 0, signatures_list = get_signames(x), ... )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot clustering centroids — plot_centroids","text":"x bascule object. types List variant types visualize. clusters List clusters visualize. cls Custom color palette signatures. sort_by Signature sort patients' exposures . exposure_thr signatures exposures greater `exposure_thr` samples highlighted. quantile_thr add signatures_list add ... Additional arguments","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot clustering centroids — plot_centroids","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the input and reconstructed mutation counts. — plot_data","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"Function visualize input reconstructed mutation counts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"","code":"plot_data( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), reconstructed = TRUE, color_by_sigs = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"x bascule object. types List variant types visualize. samples List samples visualize. clusters List clusters visualize. reconstructed Logical. `TRUE`, reconstructed counts, .e., computed alpha x beta, visualized. color_by_sigs Logical. `TRUE`, context report number mutations split signature.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the estimated exposures — plot_exposures","title":"Function to visualize the estimated exposures — plot_exposures","text":"Function visualize estimated exposures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the estimated exposures — plot_exposures","text":"","code":"plot_exposures( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), sample_name = FALSE, color_palette = NULL, add_centroid = FALSE, sort_by = NULL, exposure_thr = 0, quantile_thr = 0, signatures_list = get_signames(x) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the estimated exposures — plot_exposures","text":"x bascule object. types List variant types visualize. samples List samples visualize. clusters List clusters visualize. sample_name Logical. `TRUE`, sample names reported x axis. color_palette Custom color palette signatures. add_centroid Logical. `TRUE`, also clustering's centroids plotted. sort_by Signature sort patients' exposures . exposure_thr signatures exposures greater `exposure_thr` samples highlighted. quantile_thr add signatures_list add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the estimated exposures — plot_exposures","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Report of the fit — plot_fit","title":"Report of the fit — plot_fit","text":"Report fit","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report of the fit — plot_fit","text":"","code":"plot_fit(x)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report of the fit — plot_fit","text":"x Bascule object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report of the fit — plot_fit","text":"assembled plots","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot parameters gradients norms — plot_gradient_norms","title":"Plot parameters gradients norms — plot_gradient_norms","text":"Visualise norms parameters gradients computed inference.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot parameters gradients norms — plot_gradient_norms","text":"","code":"plot_gradient_norms(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot parameters gradients norms — plot_gradient_norms","text":"x bascule object. types List types visualise gradient norms .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot parameters gradients norms — plot_gradient_norms","text":"patchwork object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot posterior probabilities — plot_posterior_probs","title":"Plot posterior probabilities — plot_posterior_probs","text":"Plot posterior probabilities assignments.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot posterior probabilities — plot_posterior_probs","text":"","code":"plot_posterior_probs(x, samples = get_samples(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot posterior probabilities — plot_posterior_probs","text":"x bascule object samples List samples visualise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot posterior probabilities — plot_posterior_probs","text":"pheatmap object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot model selection scores — plot_scores","title":"Plot model selection scores — plot_scores","text":"Function plot model selection scores NMF variant type clustering. Reported scores BIC negative log-likelihood.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot model selection scores — plot_scores","text":"","code":"plot_scores(x, types = get_types(x), remove_outliers = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot model selection scores — plot_scores","text":"x bascule object. types List variant types visualize. remove_outliers Logical. `TRUE`, outliers score removed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot model selection scores — plot_scores","text":"ggplot2 object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the estimated and reference signatures. — plot_signatures","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"Function visualize estimated reference signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"","code":"plot_signatures( x, types = get_types(x), context = T, cls = NULL, signames = get_signames(x) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"x bascule object. types List variant types visualize. context Logical. `TRUE`, context names reported x axis. cls Custom color palette signatures. signames List signatures visualize.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"Function visualize similarity denovo reference signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"","code":"plot_similarity_reference( x, reference = NULL, type = \"SBS\", similarity_cutoff = 0.8, context = T, add_pheatmap = T )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"x Bascule object. reference External reference catalogue compare denovo . similarity_cutoff add context Logical. set TRUE, context labels reported x axis. add_pheatmap Logical. set TRUE, heatmap similarity values among signatures reported. by_subs Logical. set TRUE, similarity computed separately substitution.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Print for class 'bascule_obj'. — print.bascule_obj","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"Print class 'bascule_obj'.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"","code":"# S3 method for class 'bascule_obj' print(x, ...)"},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"x obj class 'bascule_obj'. ... Default S3 method parameter.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"Nothing.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"De novo signatures refinement. — refine_denovo_signatures","title":"De novo signatures refinement. — refine_denovo_signatures","text":"Function refine inferred de novo signatures. function performs linear combination de novo reference signatures. de novo signature can explained linear combination one reference signatures, removed exposures distributed among similar signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"De novo signatures refinement. — refine_denovo_signatures","text":"","code":"refine_denovo_signatures(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"De novo signatures refinement. — refine_denovo_signatures","text":"x bascule object. types List variant types perform de novo refinement .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"De novo signatures refinement. — refine_denovo_signatures","text":"bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis of a synthetic cohort — synthetic_data","title":"Analysis of a synthetic cohort — synthetic_data","text":"Input SBS DBS counts BASCULE fits cohort 150 samples whose counts exposures generated BASCULE generative model.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis of a synthetic cohort — synthetic_data","text":"","code":"data(synthetic_data)"},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Analysis of a synthetic cohort — synthetic_data","text":"object class list length 3.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve the name of the currently loaded environment. — which_conda_env","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"Function retrieve name currently loaded conda environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"","code":"which_conda_env()"},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"character corresponding name loaded environment.","code":""}] +[{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. 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Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https:://caravagnalab.github.io/bascule/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"package-setup","dir":"Articles","previous_headings":"","what":"Package Setup","title":"Fit on real data","text":"","code":"library(bascule) #> ✔ Loading bascule. Support : knitr::opts_chunk$set(warning = FALSE, message = FALSE) configure_environment(envname=\"bascule-env\", use_default=TRUE) py = reticulate::import(\"pybascule\")"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"model-fitting","dir":"Articles","previous_headings":"","what":"Model Fitting","title":"Fit on real data","text":", load breast tumor type fit object (breast_data) bascule package, retrieve input data (counts) loaded fit object. execute fit function using input data (counts).","code":"data(\"breast_data\") x = breast_data$x counts = get_input(x, matrix=TRUE, reconstructed=FALSE) x_pre_refinement = fit( counts=counts, k_list=0:25, cluster=15, reference_cat=breast_data$reference_cat, n_steps=3000, lr=0.005, seed_list=c(19,255,18321,331), hyperparameters=list(\"penalty_scale\"=0, \"alpha_conc\"=alpha_conc), store_fits=TRUE, py=py, CUDA=TRUE, autoguide=TRUE )"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"signature-refinement","dir":"Articles","previous_headings":"","what":"Signature Refinement","title":"Fit on real data","text":", eliminate inferred de novo signatures explainable linear combination signatures.","code":"x_refined = refine_denovo_signatures(x_pre_refinement)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"patients-re-clustering","dir":"Articles","previous_headings":"","what":"Patients Re-Clustering","title":"Fit on real data","text":"redo clustering step (applicable), using new set signatures updated exposure matrix.","code":"x = fit_clustering( x_pre_refinement, cluster=15, seed_list=c(19,255,18321,331), hyperparameters=list(\"penalty_scale\"=0, \"alpha_conc\"=alpha_conc), store_fits=TRUE, py=py, CUDA=TRUE, autoguide=TRUE ) x = x %>% merge_clusters()"},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"mutational-signatures-visualization","dir":"Articles","previous_headings":"","what":"Mutational Signatures Visualization","title":"Fit on real data","text":"","code":"plot_signatures(x)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"exposure-matrix-visualization","dir":"Articles","previous_headings":"Mutational Signatures Visualization","what":"Exposure Matrix Visualization","title":"Fit on real data","text":"","code":"plot_exposures(x) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale."},{"path":"https:://caravagnalab.github.io/bascule/articles/Fit_breast_data.html","id":"clusters-centroids-visualization","dir":"Articles","previous_headings":"Mutational Signatures Visualization","what":"Clusters Centroids Visualization","title":"Fit on real data","text":"","code":"plot_centroids(x) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale."},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"load-datasets","dir":"Articles","previous_headings":"","what":"Load datasets","title":"Inference","text":"can load data example_dataset, bascule object containing true signatures exposures used generate mutation counts matrix. object, data SBS DBS reported. can extract mutation count matrix object using get_input function. reconstructed=FALSE obtaining observed counts, reconstructed ones computed matrix multiplication exposures signatures. use reference COSMIC catalogue SBS DBS. example dataset, true number signatures five SBS DBS, thus can provide list K test values 0 7.","code":"data(\"synthetic_data\") counts = synthetic_data$counts head(counts[[\"SBS\"]][, 1:10]) #> A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T A[C>T]A #> G1_1 118 7 0 52 10 2 1 5 27 #> G1_2 236 21 5 107 17 12 3 14 67 #> G1_3 132 8 1 50 11 5 1 7 42 #> G1_4 116 15 3 40 10 6 0 12 40 #> G1_5 149 12 3 56 10 3 2 14 49 #> G1_6 161 10 2 66 13 8 4 13 62 #> A[C>T]C #> G1_1 10 #> G1_2 35 #> G1_3 19 #> G1_4 26 #> G1_5 16 #> G1_6 25 head(counts[[\"DBS\"]][, 1:10]) #> AC>CA AC>CG AC>CT AC>GA AC>GG AC>GT AC>TA AC>TG AC>TT AT>CA #> G1_1 5 1 4 8 4 12 5 0 6 13 #> G1_2 4 1 6 4 3 17 0 1 3 16 #> G1_3 5 0 4 6 1 13 1 0 2 18 #> G1_4 2 0 0 2 0 4 1 1 2 3 #> G1_5 4 0 4 3 0 6 0 1 2 8 #> G1_6 0 0 3 1 0 5 0 1 1 1 reference_cat = list(\"SBS\"=COSMIC_sbs_filt, \"DBS\"=COSMIC_dbs) K_list = 0:7"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"fit-the-model","dir":"Articles","previous_headings":"","what":"Fit the model","title":"Inference","text":"Now, can fit model. Let’s first fit NMF perform signatures deconvolution.","code":"x = fit(counts=counts, k_list=K_list, n_steps=3000, reference_cat=reference_cat, keep_sigs=c(\"SBS1\",\"SBS5\"), # force fixed signatures store_fits=TRUE, py=py) x = synthetic_data$x"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualize-the-inference-scores","dir":"Articles","previous_headings":"","what":"Visualize the inference scores","title":"Inference","text":"can inspect model selection procedure.","code":"plot_scores(x) #> Joining with `by = join_by(parname, value_fit, seed, type)` plot_gradient_norms(x)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualize-the-inferred-parameters","dir":"Articles","previous_headings":"","what":"Visualize the inferred parameters","title":"Inference","text":"can visualize inferred signatures. , notice 41 20 SBS DBS signatures, model selects 6 5 signatures catalogue. Moreover, also infers denovo signature SBS counts.","code":"plot_signatures(x)"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"post-fit-heuristics-and-clustering","dir":"Articles","previous_headings":"","what":"Post fit heuristics and clustering","title":"Inference","text":"can notice signatures plots clear similarity certain signatures. can compute linear combination de novo signatures remove similar reference ones. refined set signatures can run model perform clustering samples based exposures.","code":"x_refined = refine_denovo_signatures(x) x_refined_cluster = fit_clustering(x_refined, cluster=3) x_refined_cluster = synthetic_data$x_refined_cluster"},{"path":"https:://caravagnalab.github.io/bascule/articles/Inference.html","id":"visualise-clustering-results","dir":"Articles","previous_headings":"","what":"Visualise clustering results","title":"Inference","text":"","code":"plot_signatures(x_refined_cluster) plot_centroids(x_refined_cluster) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values. plot_exposures(x_refined_cluster) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale. #> Warning: No shared levels found between `names(values)` of the manual scale and the #> data's colour values."},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"installation-of-the-package","dir":"Articles","previous_headings":"","what":"Installation of the package","title":"bascule","text":"can install bascule GitHub using devtools. Load package.","code":"devtools::install_github(\"caravagnalab/bascule\") library(bascule)"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"python-dependencies-installation","dir":"Articles","previous_headings":"","what":"Python dependencies installation","title":"bascule","text":"package loaded, might execute configure_environment() function automatically check whether: version Anaconda Miniconda available, otherwise Miniconda installation started, conda environment loaded, package check bascule-env present, otherwise created, use existing conda environment, can loaded loading package, either reticulate function reticulate::use_condaenv() using bascule function load_conda_env(): eventually, required Python dependencies installed loaded environment, installed.","code":"reticulate::use_condaenv(\"env-name\", required=TRUE) load_conda_env(envname=\"env-name\")"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"functions-to-manually-configure-an-environment","dir":"Articles","previous_headings":"","what":"Functions to manually configure an environment","title":"bascule","text":"function configure_environment() can used interactively manually configure existing environment, create one scratch. function first check Anaconda Miniconda installation available, otherwise prompt Miniconda installation. input name environment either name existing environment name environment created. environment loaded created, required Python dependencies installed.","code":"configure_environment(env_name=\"bascule-env\", use_default=F)"},{"path":"https:://caravagnalab.github.io/bascule/articles/bascule.html","id":"check-the-loaded-python-version-and-environment","dir":"Articles","previous_headings":"","what":"Check the loaded Python version and environment","title":"bascule","text":"package provides also set helper functions check environment loaded. have_loaded_env() check environment already loaded, which_conda_env() check environment loaded. have_python_deps() check Python packages list installed specified environment. load_conda_env() load specified environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Elena Buscaroli. Author, maintainer. Azad Sadr. Author, maintainer. Giulio Caravagna. Author.","code":""},{"path":"https:://caravagnalab.github.io/bascule/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Buscaroli E, Sadr , Caravagna G (2024). bascule: bascule. R package version 0.1.0, https://caravagnalab.github.io/bascule/, https://github.com/caravagnalab/bascule.","code":"@Manual{, title = {bascule: bascule}, author = {Elena Buscaroli and Azad Sadr and Giulio Caravagna}, year = {2024}, note = {R package version 0.1.0, https://caravagnalab.github.io/bascule/}, url = {https://github.com/caravagnalab/bascule}, }"},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"bascule-","dir":"","previous_headings":"","what":"bascule","title":"bascule","text":"Bascule Bayesian model fit multiple signature types multiple patients, leveraging pre-existing catalogue known signatures COSMIC. Bascule searches known signatures input catalogue well new signatures outside catalogue, accounting hidden structure input data (e.g., distinct tumour types). Moreover, bascule performs tensor clustering retrieve latent groups input cohort exposures multiple signature types jointly. model uses non-negative matrix factorisation variational inference implemented pybascule Python package.","code":""},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"bascule","text":"use bascule, please cite: ……","code":""},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"bascule","text":"can install released version bascule GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"caravagnalab/bascule\")"},{"path":"https:://caravagnalab.github.io/bascule/index.html","id":"copyright-and-contacts","dir":"","previous_headings":"Installation","what":"Copyright and contacts","title":"bascule","text":"Elena Buscaroli, Azad Sadr, Giulio Caravagna. Cancer Data Science (CDS) Laboratory, University Trieste, Italy.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"COSMIC catalogue CN (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"","code":"data(COSMIC_cn)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_cn.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for CN (version 3.4, GRCh37) — COSMIC_cn","text":"object class data.frame 24 rows 48 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"COSMIC catalogue DBS (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"","code":"data(COSMIC_dbs)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_dbs.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for DBS (version 3.4, GRCh37) — COSMIC_dbs","text":"object class data.frame 20 rows 78 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"COSMIC catalogue Indels (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"","code":"data(COSMIC_indels)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_indels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for Indels (version 3.4, GRCh37) — COSMIC_indels","text":"object class data.frame 18 rows 83 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"COSMIC catalogue SBS (version 3.4, GRCh37)","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"","code":"data(COSMIC_sbs)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for SBS (version 3.4, GRCh37) — COSMIC_sbs","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":null,"dir":"Reference","previous_headings":"","what":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"Filtered version COSMIC catalogue. validated signatures present. signature (besides SBS5) contexts probability mass 0.02 set 0 probabilities re-normalized contexts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"","code":"data(COSMIC_sbs_filt)"},{"path":"https:://caravagnalab.github.io/bascule/reference/COSMIC_sbs_filt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COSMIC catalogue for SBS filtered (version 3.4, GRCh37) — COSMIC_sbs_filt","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":null,"dir":"Reference","previous_headings":"","what":"Degasperi DBS catalogue — Degasperi_DBS","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"DBS signatures extracted released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"","code":"data(Degasperi_DBS)"},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_DBS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Degasperi DBS catalogue — Degasperi_DBS","text":"object class data.frame 39 rows 78 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":null,"dir":"Reference","previous_headings":"","what":"Degasperi SBS catalogue — Degasperi_SBS","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"SBS signatures extracted released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"","code":"data(Degasperi_SBS)"},{"path":"https:://caravagnalab.github.io/bascule/reference/Degasperi_SBS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Degasperi SBS catalogue — Degasperi_SBS","text":"object class data.frame 120 rows 96 columns.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/bascule-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bascule: bascule — bascule-package","title":"bascule: bascule — bascule-package","text":"packages provides bascule (Bayesian inference clustering mutational signatures established catalogue) algorithm detect single-nucleotide substituion signatures cancer. bascule provides full Bayesian formulation based non-negative matrix factorisation, leveraging catalogue known signatures. tool specifically developed detect de novo mutational signatures type (SBS, DBS, IDS, ...) different pre-defined reference catalogue perform clustering samples signature types jointly.","code":""},{"path":[]},{"path":"https:://caravagnalab.github.io/bascule/reference/bascule-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bascule: bascule — bascule-package","text":"Maintainer: Elena Buscaroli ele.buscaroli@gmail.com Authors: Giulio Caravagna gcaravagn@gmail.com","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis of breast tumours — breast_data","title":"Analysis of breast tumours — breast_data","text":"Input SBS DBS counts BASCULE fits 2682 breast tumours released \"Substitution mutational signatures whole-genome–sequenced cancers UK population.\" Degasperi et al.Science 376, Issue 6591, 2022. PMID: 35949260","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis of breast tumours — breast_data","text":"","code":"data(breast_data)"},{"path":"https:://caravagnalab.github.io/bascule/reference/breast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Analysis of breast tumours — breast_data","text":"object class list length 2.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Configure the reticulate environment — configure_environment","title":"Configure the reticulate environment — configure_environment","text":"Function configure Python dependencies R. Python environment available, function check version conda miniconda, otherwise install miniconda, install Python package pybascule.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Configure the reticulate environment — configure_environment","text":"","code":"configure_environment(envname = \"bascule-env\", use_default = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/configure_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Configure the reticulate environment — configure_environment","text":"env_name name conda environment use, available.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to map de novo signatures to input catalogues — convert_dn_names","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"Function map de novo signatures input catalogues","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"","code":"convert_dn_names(x, x.simul = NULL, reference_cat = NULL, cutoff = 0.8)"},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"x Object class \"bascule_obj\" x.simul Another object class \"bascule_obj\". present, `x` de novo signatures mapped `x_simul` ones reference_cat List reference catalogues. `NULL`, `x` de novo signatures mapped catalogues. cutoff Threshold cosine similarity.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/convert_dn_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to map de novo signatures to input catalogues — convert_dn_names","text":"Modified version `x` mapped de novo names renamed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a bascule object — fit","title":"Fit a bascule object — fit","text":"Fit bascule object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a bascule object — fit","text":"","code":"fit( counts, k_list, cluster = NULL, reference_cat = list(SBS = COSMIC_filt, DBS = COSMIC_dbs), keep_sigs = c(\"SBS1\", \"SBS5\"), hyperparameters = NULL, lr = 0.005, optim_gamma = 0.1, n_steps = 3000, py = NULL, enumer = \"parallel\", nonparametric = TRUE, autoguide = FALSE, filter_dn = FALSE, min_exposure = 0.2, CUDA = TRUE, compile = FALSE, store_parameters = FALSE, store_fits = TRUE, seed_list = c(10) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a bascule object — fit","text":"counts List mutation counts matrices multiple variant types. k_list List number denovo signatures test. cluster Maximum number clusters. `NULL`, clustering performed. reference_cat List reference catalogues use NMF. Names must input counts. keep_sigs List reference signatures keep even found low exposures. hyperparameters List hyperparameters passed NMF clustering models. lr Learning rate used SVI. optim_gamma Deprecated n_steps Number iterations inference. py User-installed version pybascule package enumer Enumeration used clustering (either `parallel` `sequential`). nonparametric Deprecated. model works nonparametric way. autoguide Logical. `TRUE`, clustering model use Pyro autoguide. filter_dn Logical. `TRUE`, contexts 0.01 denovo signatures set 0, provided filtered signatures remain consistent inferred ones. min_exposure Reference signatures exposures lower `min_exposure` dropped. CUDA Logical. `TRUE` GPU available, models run GPU. compile Deprecated. store_parameters Logical. `TRUE`, parameters every step inference stored object. store_fits Logical. `TRUE`, tested fits, .e., every value `K`, stored object. seed_list List seeds used every input configuration.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a bascule object — fit","text":"Bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit clustering — fit_clustering","title":"Fit clustering — fit_clustering","text":"Fit clustering","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit clustering — fit_clustering","text":"","code":"fit_clustering( x, cluster, hyperparameters = NULL, lr = 0.005, optim_gamma = 0.1, n_steps = 3000, py = NULL, enumer = \"parallel\", nonparametric = TRUE, autoguide = TRUE, CUDA = TRUE, compile = FALSE, store_parameters = FALSE, store_fits = TRUE, seed_list = c(10) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit clustering — fit_clustering","text":"x Bascule object signatures deconvolution performed. cluster Maximum number clusters. hyperparameters List hyperparameters passed NMF clustering models. lr Learning rate SVI optimizer. optim_gamma Deprecated. n_steps Number steps inference. py User-installed version pybascule package enumer Enumeration used clustering (either `parallel` `sequential`). nonparametric Deprecated. model works nonparametric way. autoguide Logical. `TRUE`, clustering model use Pyro autoguide. CUDA Logical. `TRUE` GPU available, models run GPU. compile Deprecated. store_parameters Logical. `TRUE`, parameters every step inference stored object. store_fits Logical. `TRUE`, tested fits, .e., every value `K`, stored object. seed_list List seeds used every input configuration.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/fit_clustering.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit clustering — fit_clustering","text":"Bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get denovo signatures names — get_denovo_signames","title":"Get denovo signatures names — get_denovo_signames","text":"Get denovo signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get denovo signatures names — get_denovo_signames","text":"","code":"get_denovo_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get denovo signatures names — get_denovo_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get denovo signatures names — get_denovo_signames","text":"list de novo signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get de novo (reference) signatures — get_denovo_signatures","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"Get de novo (reference) signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"","code":"get_denovo_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_denovo_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get de novo (reference) signatures — get_denovo_signatures","text":"De novo signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"Get exposures — get_exposure","title":"Get exposures — get_exposure","text":"Get exposures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get exposures — get_exposure","text":"","code":"get_exposure( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), add_groups = FALSE, matrix = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get exposures — get_exposure","text":"x bascule object. types List variant types retrieve signames . samples List samples report exposures . clusters List cluster labels report exposures . add_groups Logical. `TRUE` add column sample's group label. matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get exposures — get_exposure","text":"Exposures matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get reference signatures names — get_fixed_signames","title":"Get reference signatures names — get_fixed_signames","text":"Get reference signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get reference signatures names — get_fixed_signames","text":"","code":"get_fixed_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get reference signatures names — get_fixed_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get reference signatures names — get_fixed_signames","text":"list reference signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get fixed (reference) signatures — get_fixed_signatures","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"Get fixed (reference) signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"","code":"get_fixed_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_fixed_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get fixed (reference) signatures — get_fixed_signatures","text":"Reference signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Get input data — get_input","title":"Get input data — get_input","text":"Get input data","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get input data — get_input","text":"","code":"get_input( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), matrix = FALSE, reconstructed = FALSE, add_groups = FALSE, by_sigs = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get input data — get_input","text":"x bascule object. types List variant types subset samples List samples subset clusters List clusters subset matrix Logical. `TRUE`, output wide format. reconstructed Logical. `TRUE`, reconstructed counts, .e., computed alpha x beta, returned. add_groups Logical. `TRUE` clustering performed, sample annotated assigned group. by_sigs Logical. `TRUE`, number mutations generated signature returned.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get input data — get_input","text":"list long wide-formatted mutations counts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":null,"dir":"Reference","previous_headings":"","what":"Get signatures names — get_signames","title":"Get signatures names — get_signames","text":"Get signatures names","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get signatures names — get_signames","text":"","code":"get_signames(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get signatures names — get_signames","text":"x bascule object. types List variant types retrieve signames .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get signatures names — get_signames","text":"list signature names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Get signatures — get_signatures","title":"Get signatures — get_signatures","text":"Get signatures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get signatures — get_signatures","text":"","code":"get_signatures(x, types = get_types(x), matrix = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get signatures — get_signatures","text":"x bascule object. types List variant types retrieve signames . matrix Logical. `TRUE`, return signatures wide format.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/get_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get signatures — get_signatures","text":"Signature matrix long wide format names names equal `types`.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if there is a loaded conda environment. — have_loaded_env","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"Function check conda environment already loaded.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"","code":"have_loaded_env()"},{"path":"https:://caravagnalab.github.io/bascule/reference/have_loaded_env.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if there is a loaded conda environment. — have_loaded_env","text":"Boolean, TRUE environment loaded, FALSE otherwise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if Python packages are installed in the environment. — have_python_deps","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"Function check one Python packages present conda environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"","code":"have_python_deps(envname = \"\", py_pkgs = c(\"pybascule\"))"},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"envname name environment check. empty, function check currently loaded environment. py_pkgs list vector Python packages.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/have_python_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if Python packages are installed in the environment. — have_python_deps","text":"list Boolean. input package, TRUE package installed, FALSE otherwise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/load_conda_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Load the input conda environment. — load_conda_env","title":"Load the input conda environment. — load_conda_env","text":"Function load input conda environment. function raise error Python version already attached reticulate package. case, necessary restart R session load desired environment **** calling lineaGT function interfacing Python - filter_dataset() fit().","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/load_conda_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load the input conda environment. — load_conda_env","text":"","code":"load_conda_env(envname = \"bascule-env\")"},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to merge similar clusters — merge_clusters","title":"Function to merge similar clusters — merge_clusters","text":"function iteratively merge clusters result similar centroid. merging stop soon cosine similarity pairs clusters `cutoff`","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to merge similar clusters — merge_clusters","text":"","code":"merge_clusters(x, cutoff = 0.8)"},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to merge similar clusters — merge_clusters","text":"x bascule object. cutoff Minimum value similarity merge two clusters.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/merge_clusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to merge similar clusters — merge_clusters","text":"bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot for class 'bascule_obj'. — plot.bascule_obj","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"default plot CNA segments wide format","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"","code":"# S3 method for class 'bascule_obj' plot(x, ...)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"x obj class 'bascule_obj'. ... Default S3 method parameter.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot.bascule_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot for class 'bascule_obj'. — plot.bascule_obj","text":"Nothing.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot clustering centroids — plot_centroids","title":"Plot clustering centroids — plot_centroids","text":"Plot clustering centroids","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot clustering centroids — plot_centroids","text":"","code":"plot_centroids( x, types = get_types(x), clusters = get_cluster_labels(x), cls = NULL, sort_by = NULL, exposure_thr = 0, quantile_thr = 0, signatures_list = get_signames(x), ... )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot clustering centroids — plot_centroids","text":"x bascule object. types List variant types visualize. clusters List clusters visualize. cls Custom color palette signatures. sort_by Signature sort patients' exposures . exposure_thr signatures exposures greater `exposure_thr` samples highlighted. quantile_thr add signatures_list add ... Additional arguments","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_centroids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot clustering centroids — plot_centroids","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the input and reconstructed mutation counts. — plot_data","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"Function visualize input reconstructed mutation counts.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"","code":"plot_data( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), reconstructed = TRUE, color_by_sigs = FALSE )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"x bascule object. types List variant types visualize. samples List samples visualize. clusters List clusters visualize. reconstructed Logical. `TRUE`, reconstructed counts, .e., computed alpha x beta, visualized. color_by_sigs Logical. `TRUE`, context report number mutations split signature.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the input and reconstructed mutation counts. — plot_data","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the estimated exposures — plot_exposures","title":"Function to visualize the estimated exposures — plot_exposures","text":"Function visualize estimated exposures","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the estimated exposures — plot_exposures","text":"","code":"plot_exposures( x, types = get_types(x), samples = get_samples(x), clusters = get_cluster_labels(x), sample_name = FALSE, color_palette = NULL, add_centroid = FALSE, sort_by = NULL, exposure_thr = 0, quantile_thr = 0, signatures_list = get_signames(x) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the estimated exposures — plot_exposures","text":"x bascule object. types List variant types visualize. samples List samples visualize. clusters List clusters visualize. sample_name Logical. `TRUE`, sample names reported x axis. color_palette Custom color palette signatures. add_centroid Logical. `TRUE`, also clustering's centroids plotted. sort_by Signature sort patients' exposures . exposure_thr signatures exposures greater `exposure_thr` samples highlighted. quantile_thr add signatures_list add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_exposures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the estimated exposures — plot_exposures","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Report of the fit — plot_fit","title":"Report of the fit — plot_fit","text":"Report fit","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report of the fit — plot_fit","text":"","code":"plot_fit(x)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report of the fit — plot_fit","text":"x Bascule object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report of the fit — plot_fit","text":"assembled plots","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot parameters gradients norms — plot_gradient_norms","title":"Plot parameters gradients norms — plot_gradient_norms","text":"Visualise norms parameters gradients computed inference.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot parameters gradients norms — plot_gradient_norms","text":"","code":"plot_gradient_norms(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot parameters gradients norms — plot_gradient_norms","text":"x bascule object. types List types visualise gradient norms .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_gradient_norms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot parameters gradients norms — plot_gradient_norms","text":"patchwork object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot posterior probabilities — plot_posterior_probs","title":"Plot posterior probabilities — plot_posterior_probs","text":"Plot posterior probabilities assignments.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot posterior probabilities — plot_posterior_probs","text":"","code":"plot_posterior_probs(x, samples = get_samples(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot posterior probabilities — plot_posterior_probs","text":"x bascule object samples List samples visualise.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_posterior_probs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot posterior probabilities — plot_posterior_probs","text":"pheatmap object","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot model selection scores — plot_scores","title":"Plot model selection scores — plot_scores","text":"Function plot model selection scores NMF variant type clustering. Reported scores BIC negative log-likelihood.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot model selection scores — plot_scores","text":"","code":"plot_scores(x, types = get_types(x), remove_outliers = FALSE)"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot model selection scores — plot_scores","text":"x bascule object. types List variant types visualize. remove_outliers Logical. `TRUE`, outliers score removed.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_scores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot model selection scores — plot_scores","text":"ggplot2 object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the estimated and reference signatures. — plot_signatures","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"Function visualize estimated reference signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"","code":"plot_signatures( x, types = get_types(x), context = T, cls = NULL, signames = get_signames(x) )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"x bascule object. types List variant types visualize. context Logical. `TRUE`, context names reported x axis. cls Custom color palette signatures. signames List signatures visualize.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the estimated and reference signatures. — plot_signatures","text":"ggplot object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"Function visualize similarity denovo reference signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"","code":"plot_similarity_reference( x, reference = NULL, type = \"SBS\", similarity_cutoff = 0.8, context = T, add_pheatmap = T )"},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"x Bascule object. reference External reference catalogue compare denovo . similarity_cutoff add context Logical. set TRUE, context labels reported x axis. add_pheatmap Logical. set TRUE, heatmap similarity values among signatures reported. by_subs Logical. set TRUE, similarity computed separately substitution.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/plot_similarity_reference.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to visualize the similarity of denovo and reference signatures. — plot_similarity_reference","text":"add","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Print for class 'bascule_obj'. — print.bascule_obj","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"Print class 'bascule_obj'.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"","code":"# S3 method for class 'bascule_obj' print(x, ...)"},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"x obj class 'bascule_obj'. ... Default S3 method parameter.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/print.bascule_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print for class 'bascule_obj'. — print.bascule_obj","text":"Nothing.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":null,"dir":"Reference","previous_headings":"","what":"De novo signatures refinement. — refine_denovo_signatures","title":"De novo signatures refinement. — refine_denovo_signatures","text":"Function refine inferred de novo signatures. function performs linear combination de novo reference signatures. de novo signature can explained linear combination one reference signatures, removed exposures distributed among similar signatures.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"De novo signatures refinement. — refine_denovo_signatures","text":"","code":"refine_denovo_signatures(x, types = get_types(x))"},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"De novo signatures refinement. — refine_denovo_signatures","text":"x bascule object. types List variant types perform de novo refinement .","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/refine_denovo_signatures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"De novo signatures refinement. — refine_denovo_signatures","text":"bascule object.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis of a synthetic cohort — synthetic_data","title":"Analysis of a synthetic cohort — synthetic_data","text":"Input SBS DBS counts BASCULE fits cohort 150 samples whose counts exposures generated BASCULE generative model.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis of a synthetic cohort — synthetic_data","text":"","code":"data(synthetic_data)"},{"path":"https:://caravagnalab.github.io/bascule/reference/synthetic_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Analysis of a synthetic cohort — synthetic_data","text":"object class list length 3.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve the name of the currently loaded environment. — which_conda_env","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"Function retrieve name currently loaded conda environment.","code":""},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"","code":"which_conda_env()"},{"path":"https:://caravagnalab.github.io/bascule/reference/which_conda_env.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve the name of the currently loaded environment. — which_conda_env","text":"character corresponding name loaded environment.","code":""}]