# Mutational Signature Comprehensive Analysis Toolkit

## Documentation for package ‘musicatk’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_flank_to_variants | Uses a genome object to find context and add it to the variant table
annotate_replication_strand | Add replication strand annotation to SBS variants based on bedgraph file
annotate_transcript_strand | Add transcript strand annotation to SBS variants (defined in genes only)
annotate_variant_length | Adds an annotation to the input musica's variant table with length of each variant
annotate_variant_type | Annotate variants with variant type ("SBS", "INS", "DEl", "DBS")
auto_predict_grid | Automatic filtering of signatures for exposure prediction gridded across specific annotation
build_custom_table | Builds a custom table from specified user variants
build_standard_table | Builds count tables using various mutation type schemas
built_tables | Retrieve the names of count_tables from a musica or musica_result object
built_tables-method | Retrieve the names of count_tables from a musica or musica_result object
cluster_exposure | Perform clustering analysis from a musica result object
combine_count_tables | Combines tables into a single table that can be used for discovery/prediction
combine_predict_grid | Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted
compare_cosmic_v2 | Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome)
compare_cosmic_v3 | Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classes
compare_results | Compare two result files to find similar signatures
cosmic_v2_sigs | COSMIC v2 SBS96 Signatures Result Object
cosmic_v2_subtype_map | Input a cancer subtype to return a list of related COSMIC signatures
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
count_table-class | 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.
create_musica | Creates a musica object from a variant table
create_umap | Create a UMAP from a musica result
dbs_musica | dbs_musica
discover_signatures | Discover mutational signatures
drop_annotation | Drops a column from the variant table that the user no longer needs
exposures | Retrieve exposures from a musica_result object
exposures-method | Retrieve exposures from a musica_result object
exposures<- | Retrieve exposures from a musica_result object
exposures<--method | Retrieve exposures from a musica_result object
exposure_differential_analysis | Compare exposures of annotated samples
extract_count_tables | Extract count tables list from a musica object
extract_variants | Extract variants from mutliple objects
extract_variants_from_maf | Extract variants from a maf object
extract_variants_from_maf_file | Extracts variants from a maf file
extract_variants_from_matrix | Extract variants from matrix or data.frame like objects
extract_variants_from_vcf | Extracts variants from a VariantAnnotation VCF object
extract_variants_from_vcf_file | Extracts variants from a vcf file
generate_result_grid | Generate result_grid from musica based on annotation and range of k
get_musica | Retrieve musica from a musica_result object
get_musica-method | Retrieve musica from a musica_result object
indel_musica | indel_musica
k_select | Plots for helping decide number of clusters
musica | musica
musica-class | The primary object that contains variants, count_tables, and samples annotations
musica_annot | musica_annot
musica_result-class | Object containing deconvolved/predicted signatures, sample weights, and the musica object the result was generated from
musica_result_grid-class | Object containing the result objects generated from the combination of annotations and a range of k values
musica_sbs96 | musica_sbs96
musica_sbs96_tiny | musica_sbs96_tiny
name_signatures | Return sample from musica object
plot_cluster | Visualize clustering results
plot_differential_analysis | Compare exposures of annotated samples
plot_exposures | Display sample exposures with bar, box, or violin plots
plot_heatmap | Plot heatmaps using the exposures matrix
plot_sample_counts | Plot distribution of sample counts
plot_sample_reconstruction_error | Plot reconstruction error for a sample
plot_signatures | Plots the mutational signatures
plot_umap | Plot a UMAP from a musica result
predict_exposure | Prediction of exposures in new samples using pre-existing signatures
rc | Reverse complement of a string using biostrings
rep_range | Replication Timing Data as GRanges Object
res | res
res_annot | res_annot
sample_names | Retrieve sample names from a musica or musica_result object
sample_names-method | Retrieve sample names from a musica or musica_result object
samp_annot | Get or set sample annotations from a musica or musica_result object
samp_annot-method | Get or set sample annotations from a musica or musica_result object
samp_annot<- | Get or set sample annotations from a musica or musica_result object
samp_annot<--method | Get or set sample annotations from a musica or musica_result object
select_genome | Helper function to load common human or mouse genomes
signatures | Retrieve signatures from a musica_result object
signatures-method | Retrieve signatures from a musica_result object
signatures<- | Retrieve signatures from a musica_result object
signatures<--method | Retrieve signatures from a musica_result object
subset_musica_by_annotation | Creates a new musica object subsetted to only one value of a sample annotation
subset_musica_by_counts | Creates a new musica subsetted to only samples with enough variants
subset_variants_by_samples | Return sample from musica_variant object
subset_variant_by_type | Subsets a variant table based on Variant Type
tables | Retrieve the list of count_tables from a musica or musica_result object
tables-method | Retrieve the list of count_tables from a musica or musica_result object
tables<- | Retrieve the list of count_tables from a musica or musica_result object
tables<--method | Retrieve the list of count_tables from a musica or musica_result object
table_selected | Retrieve table name used for plotting from a musica_result object
table_selected-method | Retrieve table name used for plotting from a musica_result object
umap | Retrieve umap list from a musica_result object
umap-method | Retrieve umap list from a musica_result object
umap<- | Retrieve umap list from a musica_result object
umap<--method | Retrieve umap list from a musica_result object
variants | Retrieve variants from a musica or musica_result object
variants-method | Retrieve variants from a musica or musica_result object
variants<- | Retrieve variants from a musica or musica_result object
variants<--method | Retrieve variants from a musica or musica_result object