Vignettes | Introduction | Installation | Setting up a musica object | Extracting variants | Choosing a genome | Creating a musica object | Creating mutation count tables | Creating a musica object directly from a count table | Discovering Signatures and Exposures | Determining an appropriate k value | Plotting | Signatures | Exposures | Comparison to external signatures (e.g. COSMIC) | Predicting exposures using pre-existing signatures | Comparing samples between groups using Sample Annotations | Adding sample annotations | Plotting exposures by a Sample Annotation | Visualizing samples in 2D using UMAP | Use of Plotly in plotting | Note on reproducibility | Session Information
Package: musicatk 2.7.1
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:
musicatk_2.7.1.tar.gz
musicatk_2.7.1.zip(r-4.7-any)musicatk_2.7.1.zip(r-4.6-any)musicatk_2.7.1.zip(r-4.5-any)
musicatk_2.7.1.tgz(r-4.6-any)musicatk_2.7.1.tgz(r-4.5-any)
musicatk_2.7.1.tar.gz(r-4.7-any)musicatk_2.7.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
musicatk/json (API)
| # Install 'musicatk' in R: |
| install.packages('musicatk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/campbio/musicatk/issues
Datasets:
- cosmic_v2_sigs - COSMIC v2 SBS96 Signatures Result Object
- cosmic_v3_dbs_sigs - COSMIC v3 DBS Genome Signatures Result Object
- cosmic_v3_indel_sigs - COSMIC v3 Indel Genome Signatures Result Object
- cosmic_v3_sbs_sigs - COSMIC v3 SBS96 Genome Signatures Result Object
- cosmic_v3_sbs_sigs_exome - COSMIC v3 SBS96 Exome Signatures Result Object
- dbs_musica - Dbs_musica
- example_predicted_exp - Example_predicted_exp
- example_predicted_sigs - Example_predicted_sigs
- full_benchmark_example - Full_benchmark_example
- indel_musica - Indel_musica
- musica - Musica
- musica_annot - Musica_annot
- musica_sbs96 - Musica_sbs96
- musica_sbs96_tiny - Musica_sbs96_tiny
- rep_range - Replication Timing Data as GRanges Object
- res - Res
- res_annot - Res_annot
- synthetic_breast_counts - Synthetic_breast_counts
- synthetic_breast_true_exposures - Synthetic_breast_true_exposures
On BioConductor:musicatk-2.7.0(bioc 3.24)musicatk-2.6.0(bioc 3.23)
softwarebiologicalquestionsomaticmutationvariantannotation
Last updated from:02bbf57e91. Checks:1 WARNING, 7 NOTE, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 503 | ||
| linux-devel | NOTE | 1238 | ||
| source / vignettes | OK | 840 | ||
| linux-release | NOTE | 1238 | ||
| macos-release | NOTE | 822 | ||
| macos-oldrel | NOTE | 843 | ||
| windows-devel | NOTE | 862 | ||
| windows-release | NOTE | 639 | ||
| windows-oldrel | NOTE | 947 | ||
| wasm-release | FAIL | 351 |
Exports:%>%add_flank_to_variantsadd_resultadjustment_thresholdadjustment_threshold<-annotate_replication_strandannotate_transcript_strandannotate_variant_lengthannotate_variant_typeauto_predict_gridbenchmarkbenchmark_get_comparisonbenchmark_get_entrybenchmark_get_predictionbenchmark_plot_comparisonbenchmark_plot_composite_exposuresbenchmark_plot_duplicate_exposuresbenchmark_plot_exposuresbenchmark_plot_signaturesbuild_custom_tablebuild_standard_tablebuilt_tablescluster_exposurecombine_count_tablescombine_predict_gridcompare_cosmic_v2compare_cosmic_v3compare_k_valscompare_resultscosmic_v2_subtype_mapcreate_benchmarkcreate_musica_from_countscreate_musica_from_variantscreate_umapcredible_intervalscredible_intervals<-descriptiondescription<-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_filefinal_comparisonfinal_comparison<-final_predfinal_pred<-generate_result_gridget_count_tableget_modalityget_modelget_result_list_entryground_truthground_truth<-hyperparameterhyperparameter<-indv_benchmarksindv_benchmarks<-initial_comparisoninitial_comparison<-initial_predinitial_pred<-intermediate_comparisonintermediate_comparison<-intermediate_predintermediate_pred<-k_selectmethod_idmethod_id<-method_view_summarymethod_view_summary<-metricsmetrics<-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_and_benchmarkpredict_exposurercresult_listresult_list<-samp_annotsamp_annot<-sample_namesselect_genomesig_view_summarysig_view_summary<-signaturessignatures<-single_summarysingle_summary<-subset_musica_by_annotationsubset_musica_by_countssubset_variant_by_typesubset_variants_by_samplestable_selectedtablestables<-thresholdthreshold<-umapumap<-variantsvariants<-
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroomBSgenomeBSgenome.Hsapiens.UCSC.hg19BSgenome.Hsapiens.UCSC.hg38BSgenome.Mmusculus.UCSC.mm10BSgenome.Mmusculus.UCSC.mm9bslibcachemcallrcarcarDatacellrangercigarillocirclizeclicliprclueclustercodetoolscolorspacecombinatcommonmarkComplexHeatmapconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdecompTumor2SigDelayedArraydendextendDerivdigestDNAcopydoBydoParalleldplyrdqrngDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapflashClustFNNfontawesomeforcatsforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgarglegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggseqlogoggsignifGlobalOptionsgluegoogledrivegooglesheets4gridBasegridExtragtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttpuvhttridsIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelme4lmtestlseilubridatemaftoolsmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmatrixTestsMCMCprecisionmemoisemgcvmimeminqamodelrmodeltoolsmultcompViewmvtnormnlmenloptrNLPNMFnnetnumDerivopensslotelpbkrtestpheatmapphilentropypillarpkgconfigplotlyplyrpngpolynompoormanprettyunitsprocessxprogresspromisespspurrrquadprogquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppParallelRcppProgressRCurlRdpackreadrreadxlreformulasregistryrematchrematch2reprexreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSpectraRSQLiterstatixrstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesscatterplot3dselectrSeqinfoshapeshinyshowtextshowtextdbsitmoslamsnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssysfontssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetimeDatetinytextmtopicmodelsTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenetzdbUCSC.utilsurcautf8uuiduwotVariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Uses a genome object to find context and add it to the variant table | add_flank_to_variants |
| Load an external model into a musica object | add_result |
| Retrieve the adjustment_threshold from a single_benchmark object | adjustment_threshold adjustment_threshold,single_benchmark-method adjustment_threshold<- adjustment_threshold<-,single_benchmark,numeric-method |
| Add replication strand annotation to SBS variants based on bedgraph file | annotate_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 variant | annotate_variant_length |
| Annotate variants with variant type ("SBS", "INS", "DEl", "DBS") | annotate_variant_type |
| Automatic filtering of signatures for exposure prediction gridded across specific annotation | auto_predict_grid |
| Run the benchmark framework on a prediction | benchmark |
| Get benchmark comparison table | benchmark_get_comparison |
| Get a single_benchmark object | benchmark_get_entry |
| Get a benchmark prediction | benchmark_get_prediction |
| Plot a signature comparison from a benchmarking analysis | benchmark_plot_comparison |
| Plot effect of composite correction | benchmark_plot_composite_exposures |
| Plot effect of duplicate correction | benchmark_plot_duplicate_exposures |
| Plot exposure comparison from a benchmarking analysis | benchmark_plot_exposures |
| Plot signatures from a benchmarking analysis | benchmark_plot_signatures |
| Builds a custom table from specified user variants | build_custom_table |
| Builds count tables using various mutation type schemas | build_standard_table |
| Retrieve the names of count_tables from a musica object | built_tables built_tables,musica-method |
| Perform clustering analysis from a musica result object | cluster_exposure |
| Combines tables into a single table that can be used for discovery/prediction | combine_count_tables |
| Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predicted | combine_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 classes | compare_cosmic_v3 |
| Compare k values | compare_k_vals |
| Compare two result files to find similar signatures | compare_results |
| COSMIC v2 SBS96 Signatures Result Object | cosmic_v2_sigs |
| Input a cancer subtype to return a list of related COSMIC signatures | cosmic_v2_subtype_map |
| COSMIC v3 DBS Genome Signatures Result Object | cosmic_v3_dbs_sigs |
| COSMIC v3 Indel Genome Signatures Result Object | cosmic_v3_indel_sigs |
| COSMIC v3 SBS96 Genome Signatures Result Object | cosmic_v3_sbs_sigs |
| COSMIC v3 SBS96 Exome Signatures Result Object | cosmic_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 |
| Create a full_benchmark object | create_benchmark |
| Creates a musica object from a mutation count table | create_musica_from_counts |
| Creates a musica object from a variant table | create_musica_from_variants |
| Create a UMAP from a model result | create_umap |
| Retrieve credible_intervals from a result_model, result_collection, or musica object | credible_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_musica | dbs_musica |
| Retrieve the description from a single_benchmark object | description description,single_benchmark-method description<- description<-,single_benchmark,CharOrNULL-method |
| Discover mutational signatures | discover_signatures |
| Drops a column from the variant table that the user no longer needs | drop_annotation |
| example_predicted_exp | example_predicted_exp |
| example_predicted_sigs | example_predicted_sigs |
| Compare exposures of annotated samples | exposure_differential_analysis |
| Retrieve exposures from a result_model, result_collection, or musica object | exposures 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 object | extract_count_tables |
| Extract variants from mutliple objects | extract_variants |
| Extract variants from a maf object | extract_variants_from_maf |
| Extracts variants from a maf file | extract_variants_from_maf_file |
| Extract variants from matrix or data.frame like objects | extract_variants_from_matrix |
| Extracts variants from a VariantAnnotation VCF object | extract_variants_from_vcf |
| Extracts variants from a vcf file | extract_variants_from_vcf_file |
| Retrieve final comparison between the prediction and the ground truth from a single_benchmark object | final_comparison final_comparison,single_benchmark-method final_comparison<- final_comparison<-,single_benchmark,data.frame-method |
| Retrieve final prediction from a single_benchmark object | final_pred final_pred,single_benchmark-method final_pred<- final_pred<-,single_benchmark,result_model-method |
| full_benchmark_example | full_benchmark_example |
| Object that contains information for a full benchmarking analysis where multiple predictions may be benchmarked | full_benchmark-class |
| Generate result_grid from musica based on annotation and range of k | generate_result_grid |
| Retrieve count_table matrix from count_table object | get_count_table |
| Retrieve a specific modality entry from a musica or result_collection object | get_modality get_modality,musica-method get_modality,result_collection-method |
| Retrieve model from a musica or result collection object | get_model get_model,musica-method get_model,result_collection-method |
| Retrieve result_list entry from a musica object | get_result_list_entry get_result_list_entry,musica,character-method |
| Retrieve the ground_truth from a full_benchmark object | ground_truth ground_truth,full_benchmark-method ground_truth<- ground_truth<-,full_benchmark,musica-method |
| Retrieve hyperparameter from a musica or result_collection object | hyperparameter hyperparameter,musica-method hyperparameter,result_collection-method hyperparameter<- hyperparameter<-,musica,list-method hyperparameter<-,result_collection,list-method |
| indel_musica | indel_musica |
| Retrieve the indv_benchmarks list from a full_benchmark object | indv_benchmarks indv_benchmarks,full_benchmark-method indv_benchmarks<- indv_benchmarks<-,full_benchmark,list-method |
| Retrieve initial comparison between the prediction and the ground truth from a single_benchmark object | initial_comparison initial_comparison,single_benchmark-method initial_comparison<- initial_comparison<-,single_benchmark,data.frame-method |
| Retrieve initial prediction from a single_benchmark object | initial_pred initial_pred,single_benchmark-method initial_pred<- initial_pred<-,single_benchmark,result_model-method |
| Retrieve intermediate comparison between the prediction and the ground truth from a single_benchmark object | intermediate_comparison intermediate_comparison,single_benchmark-method intermediate_comparison<- intermediate_comparison<-,single_benchmark,data.frame-method |
| Retrieve intermediate prediction from a single_benchmark object | intermediate_pred intermediate_pred,single_benchmark-method intermediate_pred<- intermediate_pred<-,single_benchmark,result_model-method |
| Plots for helping decide number of clusters | k_select |
| Retrieve the method id from a single_benchmark object | method_id method_id,single_benchmark-method method_id<- method_id<-,single_benchmark,character-method |
| Retrieve the method_view_summary from a full_benchmark object | method_view_summary method_view_summary,full_benchmark-method method_view_summary<- method_view_summary<-,full_benchmark,matrix-method |
| Retrieve metrics from a result_model, result_collection, or musica object | metrics 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 object | modality modality,musica-method 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 object | 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 |
| musica | musica |
| musica_annot | musica_annot |
| musica_sbs96 | musica_sbs96 |
| musica_sbs96_tiny | musica_sbs96_tiny |
| The primary object that contains variants, count_tables, and samples annotations | musica-class |
| Starts the musicatk interactive Shiny app | musicatk |
| Rename signatures for a model | name_signatures |
| Retrieve num_signatures from a result_model, result_collection, or musica object | num_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 object | other_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 object | parameter parameter,musica-method parameter,result_collection-method parameter<- parameter<-,musica,list-method parameter<-,result_collection,list-method |
| Visualize clustering results | plot_cluster |
| Compare exposures of annotated samples | plot_differential_analysis |
| Display sample exposures with bar, box, or violin plots | plot_exposures |
| Plot heatmaps using the exposures matrix | plot_heatmap |
| Plot k comparison | plot_k_comparison |
| Plot distribution of sample counts | plot_sample_counts |
| Plot reconstruction error for a sample | plot_sample_reconstruction_error |
| Plots the mutational signatures | plot_signatures |
| Plot a UMAP from a musica result | plot_umap |
| Predict and benchmark | predict_and_benchmark |
| Prediction of exposures in new samples using pre-existing signatures | predict_exposure |
| Reverse complement of a string using biostrings | rc |
| Replication Timing Data as GRanges Object | rep_range |
| res | res |
| res_annot | res_annot |
| The Result Collection object that contains modality, input parameters, prior hyperparameters | result_collection-class |
| Retrieve result_list from a musica object | result_list result_list,musica-method result_list<- result_list<-,musica,SimpleList-method |
| Object that contains results for a single model | result_model-class |
| Get or set sample annotations from a musica object | samp_annot samp_annot,musica-method samp_annot<- samp_annot<-,musica,character,vector-method |
| Retrieve sample names from a musica object | sample_names sample_names,musica-method |
| Helper function to load common human or mouse genomes | select_genome |
| Retrieve the sig_view_summary from a full_benchmark object | sig_view_summary sig_view_summary,full_benchmark-method sig_view_summary<- sig_view_summary<-,full_benchmark,matrix-method |
| Retrieve signatures from a result_model, result_collection, or musica object | signatures 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 |
| Object that contains information for an individual benchmark run | single_benchmark-class |
| Retrieve the single summary matrix from a single_benchmark object | single_summary single_summary,single_benchmark-method single_summary<- single_summary<-,single_benchmark,matrix-method |
| Creates a new musica object subsetted to only one value of a sample annotation | subset_musica_by_annotation |
| Creates a new musica subsetted to only samples with enough variants | subset_musica_by_counts |
| Subsets a variant table based on Variant Type | subset_variant_by_type |
| Return sample from musica_variant object | subset_variants_by_samples |
| synthetic_breast_counts | synthetic_breast_counts |
| synthetic_breast_true_exposures | synthetic_breast_true_exposures |
| Retrieve table name used for plotting from a result_model object | table_selected table_selected,result_model-method |
| Retrieve the list of count_tables from a musica object | tables tables,musica-method tables<- tables<-,musica,list-method |
| Retrieve the threshold from a single_benchmark object | threshold threshold,single_benchmark-method threshold<- threshold<-,single_benchmark,numeric-method |
| Retrieve umap list from a result_model, result_collection, or musica object | umap 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 object | variants variants,musica-method variants<- variants<-,musica,data.table-method |
