Man pages for musicatk
Mutational Signature Comprehensive Analysis Toolkit

add_flank_to_variantsUses a genome object to find context and add it to the...
add_variant_typeGenerates a variant type table
annotate_replication_strandAdd replication strand annotation to SBS variants based on...
annotate_transcript_strandAdd transcript strand annotation to SBS variants (defined in...
annotate_variant_lengthAdds an annotation to the input musica's variant table with...
annotate_variant_typeAnnotate variants with variant type ("SBS", "INS", "DEl",...
auto_predict_gridAutomatic filtering of signatures for exposure prediction...
auto_subset_sigsAutomatic filtering of inactive signatures
build_custom_tableBuilds a custom table from specified user variants
build_standard_tableBuilds count tables using various mutation type schemas
combine_count_tablesCombines tables into a single table that can be used for...
combine_predict_gridCombine prediction grid list into a result object. Exposure...
compare_cosmic_v2Compare a result object to COSMIC V2 SBS Signatures...
compare_cosmic_v3Compare a result object to COSMIC V3 Signatures; Select exome...
compare_resultsCompare two result files to find similar signatures
cosmic_v2_sigsCOSMIC v2 SBS96 Signatures Result Object
cosmic_v2_subtype_mapInput a cancer subtype to return a list of related COSMIC...
cosmic_v3_dbs_sigsCOSMIC v3 DBS Genome Signatures Result Object
cosmic_v3_indel_sigsCOSMIC v3 Indel Genome Signatures Result Object
cosmic_v3_sbs_sigsCOSMIC v3 SBS96 Genome Signatures Result Object
cosmic_v3_sbs_sigs_exomeCOSMIC v3 SBS96 Exome Signatures Result Object
count_table-classObject containing the count table matrices, their names and...
create_dbs_tableCreates and adds a table for standard doublet base...
create_musicaCreates a musica object from a variant table
create_sbs192_tableUses a genome object to find context and generate standard...
create_sbs96_tableUses a genome object to find context and generate standard...
create_umapCreate a UMAP from a musica result
dbs_musicadbs_musica
discover_signaturesDiscover mutational signatures
dot-jsdCalculates 1 - Jensen-Shannon Divergences between all pairs...
drop_annotationDrops a column from the variant table that the user no longer...
exposuresRetrieve exposures from a musica_result object
extract_count_tablesExtract count tables list from a musica object
extract_variantsExtract variants from mutliple objects
extract_variants_from_mafExtract variants from a maf object
extract_variants_from_maf_fileExtracts variants from a maf file
extract_variants_from_matrixExtract variants from matrix or data.frame like objects
extract_variants_from_vcfExtracts variants from a VariantAnnotation VCF object
extract_variants_from_vcf_fileExtracts variants from a vcf file
generate_result_gridGenerate result_grid from musica based on annotation and...
indel_musicaindel_musica
musicaRetrieve musica from a musica_result object
musica_annotmusica_annot
musica-classThe primary object that contains variants, count_tables, and...
musica_result-classObject containing deconvolved/predicted signatures, sample...
musica_result_grid-classObject containing the result objects generated from the...
musica_sbs96musica_sbs96
musica_sbs96_tinymusica_sbs96_tiny
name_signaturesReturn sample from musica object
pipePipe operator
plot_exposuresDisplay sample exposures with bar, box, or violin plots
plot_sample_countsPlot distribution of sample counts
plot_sample_reconstruction_errorPlot reconstruction error for a sample
plot_signaturesPlots the mutational signatures
plot_umapPlot a UMAP from a musica result
predict_exposurePrediction of exposures in new samples using pre-existing...
rcReverse complement of a string using biostrings
rep_rangeReplication Timing Data as GRanges Object
resres
res_annotres_annot
samp_annotGet or set sample annotations from a musica or musica_result...
sample_namesRetrieve sample names from a musica or musica_result object
select_genomeHelper function to load common human or mouse genomes
signaturesRetrieve signatures from a musica_result object
subset_musica_by_annotationCreates a new musica object subsetted to only one value of a...
subset_musica_by_countsCreates a new musica subsetted to only samples with enough...
subset_variant_by_typeSubsets a variant table based on Variant Type
subset_variants_by_samplesReturn sample from musica_variant object
table_96Generates a 96 motif table based on input counts for plotting
table_nameRetrieve table name used for plotting from a musica_result...
tablesRetrieve the list of count_tables from a musica or...
umapRetrieve umap list from a musica_result object
variantsRetrieve variants from a musica or musica_result object
musicatk documentation built on Nov. 8, 2020, 5:16 p.m.