Package: musicatk 2.1.0

Joshua D. Campbell

musicatk: Mutational Signature Comprehensive Analysis Toolkit

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Authors:Aaron Chevalier [aut], Natasha Gurevich [aut], Tao Guo [aut], Joshua D. Campbell [aut, cre]

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musicatk.pdf |musicatk.html✨
musicatk/json (API)
NEWS

# Install 'musicatk' in R:
install.packages('musicatk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/campbio/musicatk/issues

Datasets:

On BioConductor:musicatk-1.99.3(bioc 3.20)musicatk-1.14.1(bioc 3.19)

softwarebiologicalquestionsomaticmutationvariantannotation

6.85 score 12 stars 17 scripts 238 downloads 88 exports 253 dependencies

Last updated 23 days agofrom:45539aac94. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 06 2024
R-4.3-macERROROct 06 2024

Exports:%>%add_flank_to_variantsannotate_replication_strandannotate_transcript_strandannotate_variant_lengthannotate_variant_typeauto_predict_gridbuild_custom_tablebuild_standard_tablebuilt_tablescluster_exposurecombine_count_tablescombine_predict_gridcompare_cosmic_v2compare_cosmic_v3compare_k_valscompare_resultscosmic_v2_subtype_mapcreate_musica_from_countscreate_musica_from_variantscreate_result_modelcreate_umapcredible_intervalscredible_intervals<-discover_signaturesdrop_annotationexposure_differential_analysisexposuresexposures<-extract_count_tablesextract_variantsextract_variants_from_mafextract_variants_from_maf_fileextract_variants_from_matrixextract_variants_from_vcfextract_variants_from_vcf_filegenerate_result_gridget_count_tableget_modalityget_modelget_result_list_entryhyperparameterhyperparameter<-k_selectmetricsmetrics<-modalitymodality<-model_idmodel_id<-musicatkname_signaturesnum_signaturesnum_signatures<-other_parametersother_parameters<-parameterparameter<-plot_clusterplot_differential_analysisplot_exposuresplot_heatmapplot_k_comparisonplot_sample_countsplot_sample_reconstruction_errorplot_signaturesplot_umappredict_exposurercresult_listresult_list<-samp_annotsamp_annot<-sample_namesselect_genomesignaturessignatures<-subset_musica_by_annotationsubset_musica_by_countssubset_variant_by_typesubset_variants_by_samplestable_selectedtablestables<-umapumap<-variantsvariants<-

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroomBSgenomeBSgenome.Hsapiens.UCSC.hg19BSgenome.Hsapiens.UCSC.hg38BSgenome.Mmusculus.UCSC.mm10BSgenome.Mmusculus.UCSC.mm9bslibcachemcallrcarcarDatacellrangercirclizeclicliprclueclustercodetoolscolorspacecombinatcommonmarkComplexHeatmapconclustconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdecompTumor2SigDelayedArraydendextendDerivdigestDNAcopydoBydoParalleldplyrdqrngDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustFNNfontawesomeforcatsforeachformatRFormulafsfutile.loggerfutile.optionsgarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggseqlogoggsignifGlobalOptionsgluegoogledrivegooglesheets4gridBasegridExtragtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttpuvhttridsIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelme4lubridatemaftoolsmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmatrixTestsMCMCprecisionmemoisemgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompViewmunsellmvtnormnlmenloptrNLPNMFnnetnumDerivopensslpbkrtestpheatmapphilentropypillarpkgconfigplogrplotlyplyrpngpolynompoormanprettyunitsprocessxprogresspromisespspurrrquadprogquantregR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRCurlreadrreadxlregistryrematchrematch2reprexreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSpectraRSQLiterstatixrstudioapirtracklayerrvestS4ArraysS4Vectorssassscalesscatterplot3dselectrshapeshinysitmoslamsnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextmtopicmodelsTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenetzdbUCSC.utilsutf8uuiduwotVariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc

Mutational Signature Comprehensive Analysis Toolkit

Aaron Chevalier, Joshua Campbell

Rendered frommusicatk.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-22
Started: 2020-10-02

Readme and manuals

Help Manual

Help pageTopics
Uses a genome object to find context and add it to the variant tableadd_flank_to_variants
Add replication strand annotation to SBS variants based on bedgraph fileannotate_replication_strand
Add transcript strand annotation to SBS variants (defined in genes only)annotate_transcript_strand
Adds an annotation to the input musica's variant table with length of each variantannotate_variant_length
Annotate variants with variant type ("SBS", "INS", "DEl", "DBS")annotate_variant_type
Automatic filtering of signatures for exposure prediction gridded across specific annotationauto_predict_grid
Builds a custom table from specified user variantsbuild_custom_table
Builds count tables using various mutation type schemasbuild_standard_table
Retrieve the names of count_tables from a musica objectbuilt_tables built_tables,musica-method
Perform clustering analysis from a musica result objectcluster_exposure
Combines tables into a single table that can be used for discovery/predictioncombine_count_tables
Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predictedcombine_predict_grid
Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome)compare_cosmic_v2
Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classescompare_cosmic_v3
Compare k valuescompare_k_vals
Compare two result files to find similar signaturescompare_results
COSMIC v2 SBS96 Signatures Result Objectcosmic_v2_sigs
Input a cancer subtype to return a list of related COSMIC signaturescosmic_v2_subtype_map
COSMIC v3 DBS Genome Signatures Result Objectcosmic_v3_dbs_sigs
COSMIC v3 Indel Genome Signatures Result Objectcosmic_v3_indel_sigs
COSMIC v3 SBS96 Genome Signatures Result Objectcosmic_v3_sbs_sigs
COSMIC v3 SBS96 Exome Signatures Result Objectcosmic_v3_sbs_sigs_exome
Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures.count_table-class
Creates a musica object from a mutation count tablecreate_musica_from_counts
Creates a musica object from a variant tablecreate_musica_from_variants
Load an external model into a result_model objectcreate_result_model
Create a UMAP from a model resultcreate_umap
Retrieve credible_intervals from a result_model, result_collection, or musica objectcredible_intervals credible_intervals,musica-method credible_intervals,result_collection-method credible_intervals,result_model-method credible_intervals<- credible_intervals<-,musica,matrix-method credible_intervals<-,result_collection,matrix-method credible_intervals<-,result_model,matrix-method
dbs_musicadbs_musica
Discover mutational signaturesdiscover_signatures
Drops a column from the variant table that the user no longer needsdrop_annotation
Compare exposures of annotated samplesexposure_differential_analysis
Retrieve exposures from a result_model, result_collection, or musica objectexposures exposures,musica-method exposures,result_collection-method exposures,result_model-method exposures<- exposures<-,musica,matrix-method exposures<-,result_collection,matrix-method exposures<-,result_model,matrix-method
Extract count tables list from a musica objectextract_count_tables
Extract variants from mutliple objectsextract_variants
Extract variants from a maf objectextract_variants_from_maf
Extracts variants from a maf fileextract_variants_from_maf_file
Extract variants from matrix or data.frame like objectsextract_variants_from_matrix
Extracts variants from a VariantAnnotation VCF objectextract_variants_from_vcf
Extracts variants from a vcf fileextract_variants_from_vcf_file
Generate result_grid from musica based on annotation and range of kgenerate_result_grid
Retrieve count_table matrix from count_table objectget_count_table
Retrieve a specific modality entry from a musica or result_collection objectget_modality get_modality,musica-method get_modality,result_collection-method
Retrieve model from a musica or result collection objectget_model get_model,musica-method get_model,result_collection-method
Retrieve result_list entry from a musica objectget_result_list_entry get_result_list_entry,musica,character-method
Retrieve hyperparameter from a musica or result_collection objecthyperparameter hyperparameter,musica-method hyperparameter,result_collection-method hyperparameter<- hyperparameter<-,musica,list-method hyperparameter<-,result_collection,list-method
indel_musicaindel_musica
Plots for helping decide number of clustersk_select
Retrieve metrics from a result_model, result_collection, or musica objectmetrics metrics,musica-method metrics,result_collection-method metrics,result_model-method metrics<- metrics<-,musica,SimpleList-method metrics<-,result_collection,SimpleList-method metrics<-,result_model,SimpleList-method
Retrieve modality from a result_model, result_collection, or musica objectmodality modality,result_collection-method modality,result_model-method modality<- modality<-,musica,matrix-method modality<-,result_collection,matrix-method modality<-,result_model,matrix-method
Retrieve model_id from a result_model, result_collection, or musica objectmodality,musica-method model_id model_id,musica-method model_id,result_collection-method model_id,result_model-method model_id<- model_id<-,musica,matrix-method model_id<-,result_collection,matrix-method model_id<-,result_model,matrix-method
musicamusica
musica_annotmusica_annot
musica_sbs96musica_sbs96
musica_sbs96_tinymusica_sbs96_tiny
The primary object that contains variants, count_tables, and samples annotationsmusica-class
Starts the musicatk interactive Shiny appmusicatk
Rename signatures for a modelname_signatures
Retrieve num_signatures from a result_model, result_collection, or musica objectnum_signatures num_signatures,musica-method num_signatures,result_collection-method num_signatures,result_model-method num_signatures<- num_signatures<-,musica,matrix-method num_signatures<-,result_collection,matrix-method num_signatures<-,result_model,matrix-method
Retrieve other_parameters from a result_model, result_collection, or musica objectother_parameters other_parameters,musica-method other_parameters,result_collection-method other_parameters,result_model-method other_parameters<- other_parameters<-,musica,matrix-method other_parameters<-,result_collection,matrix-method other_parameters<-,result_model,matrix-method
Retrieve parameter from a musica or result_collection objectparameter parameter,musica-method parameter,result_collection-method parameter<- parameter<-,musica,list-method parameter<-,result_collection,list-method
Visualize clustering resultsplot_cluster
Compare exposures of annotated samplesplot_differential_analysis
Display sample exposures with bar, box, or violin plotsplot_exposures
Plot heatmaps using the exposures matrixplot_heatmap
Plot k comparisonplot_k_comparison
Plot distribution of sample countsplot_sample_counts
Plot reconstruction error for a sampleplot_sample_reconstruction_error
Plots the mutational signaturesplot_signatures
Plot a UMAP from a musica resultplot_umap
Prediction of exposures in new samples using pre-existing signaturespredict_exposure
Reverse complement of a string using biostringsrc
Replication Timing Data as GRanges Objectrep_range
resres
res_annotres_annot
The Result Collection object that contains modality, input parameters, prior hyperparametersresult_collection-class
Retrieve result_list from a musica objectresult_list result_list,musica-method result_list<- result_list<-,musica,SimpleList-method
Object that contains results for a single modelresult_model-class
Get or set sample annotations from a musica objectsamp_annot samp_annot,musica-method samp_annot<- samp_annot<-,musica,character,vector-method
Retrieve sample names from a musica objectsample_names sample_names,musica-method
Helper function to load common human or mouse genomesselect_genome
Retrieve signatures from a result_model, result_collection, or musica objectsignatures signatures,musica-method signatures,result_collection-method signatures,result_model-method signatures<- signatures<-,musica,matrix-method signatures<-,result_collection,matrix-method signatures<-,result_model,matrix-method
Creates a new musica object subsetted to only one value of a sample annotationsubset_musica_by_annotation
Creates a new musica subsetted to only samples with enough variantssubset_musica_by_counts
Subsets a variant table based on Variant Typesubset_variant_by_type
Return sample from musica_variant objectsubset_variants_by_samples
Retrieve table name used for plotting from a result_model objecttable_selected table_selected,result_model-method
Retrieve the list of count_tables from a musica objecttables tables,musica-method tables<- tables<-,musica,list-method
Retrieve umap list from a result_model, result_collection, or musica objectumap umap,musica-method umap,result_collection-method umap,result_model-method umap<- umap<-,musica,matrix-method umap<-,result_collection,matrix-method umap<-,result_model,matrix-method
Retrieve variants from a musica objectvariants variants,musica-method variants<- variants<-,musica,data.table-method