# Mutational Signature Comprehensive Analysis Toolkit

## Documentation for package ‘musicatk’ version 2.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E G H I K M N O P R S T U V

## -- A --

add_flank_to_variants | Uses a genome object to find context and add it to the variant table
add_result | Load an external model into a musica object
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

## -- B --

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 object
built_tables-method | Retrieve the names of count_tables from a musica object

## -- C --

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 signatures and exposures of different models. 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_k_vals | Compare k values
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_from_counts | Creates a musica object from a mutation count table
create_musica_from_variants | Creates a musica object from a variant table
create_umap | Create a UMAP from a model result
credible_intervals | Retrieve credible_intervals from a result_model, result_collection, or musica object
credible_intervals-method | Retrieve credible_intervals from a result_model, result_collection, or musica object
credible_intervals<- | Retrieve credible_intervals from a result_model, result_collection, or musica object
credible_intervals<--method | Retrieve credible_intervals from a result_model, result_collection, or musica object

## -- D --

dbs_musica | dbs_musica
discover_signatures | Discover mutational signatures
drop_annotation | Drops a column from the variant table that the user no longer needs

## -- E --

exposures | Retrieve exposures from a result_model, result_collection, or musica object
exposures-method | Retrieve exposures from a result_model, result_collection, or musica object
exposures<- | Retrieve exposures from a result_model, result_collection, or musica object
exposures<--method | Retrieve exposures from a result_model, result_collection, or musica 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

## -- G --

generate_result_grid | Generate result_grid from musica based on annotation and range of k
get_count_table | Retrieve count_table matrix from count_table object
get_modality | Retrieve a specific modality entry from a musica or result_collection object
get_modality-method | Retrieve a specific modality entry from a musica or result_collection object
get_model | Retrieve model from a musica or result collection object
get_model-method | Retrieve model from a musica or result collection object
get_result_list_entry | Retrieve result_list entry from a musica object
get_result_list_entry-method | Retrieve result_list entry from a musica object

## -- H --

hyperparameter | Retrieve hyperparameter from a musica or result_collection object
hyperparameter-method | Retrieve hyperparameter from a musica or result_collection object
hyperparameter<- | Retrieve hyperparameter from a musica or result_collection object
hyperparameter<--method | Retrieve hyperparameter from a musica or result_collection object

## -- I --

indel_musica | indel_musica

## -- K --

k_select | Plots for helping decide number of clusters

## -- M --

metrics | Retrieve metrics from a result_model, result_collection, or musica object
metrics-method | Retrieve metrics from a result_model, result_collection, or musica object
metrics<- | Retrieve metrics from a result_model, result_collection, or musica object
metrics<--method | Retrieve metrics from a result_model, result_collection, or musica object
modality | Retrieve modality from a result_model, result_collection, or musica object
modality-method | Retrieve modality from a result_model, result_collection, or musica object
modality<- | Retrieve modality from a result_model, result_collection, or musica object
modality<--method | Retrieve modality from a result_model, result_collection, or musica object
model_id | Retrieve model_id from a result_model, result_collection, or musica object
model_id-method | Retrieve model_id from a result_model, result_collection, or musica object
model_id<- | Retrieve model_id from a result_model, result_collection, or musica object
model_id<--method | Retrieve model_id from a result_model, result_collection, or musica object
musica | musica
musica-class | The primary object that contains variants, count_tables, and samples annotations
musicatk | Starts the musicatk interactive Shiny app
musica_annot | musica_annot
musica_sbs96 | musica_sbs96
musica_sbs96_tiny | musica_sbs96_tiny

## -- N --

name_signatures | Rename signatures for a model
num_signatures | Retrieve num_signatures from a result_model, result_collection, or musica object
num_signatures-method | Retrieve num_signatures from a result_model, result_collection, or musica object
num_signatures<- | Retrieve num_signatures from a result_model, result_collection, or musica object
num_signatures<--method | Retrieve num_signatures from a result_model, result_collection, or musica object

## -- O --

other_parameters | Retrieve other_parameters from a result_model, result_collection, or musica object
other_parameters-method | Retrieve other_parameters from a result_model, result_collection, or musica object
other_parameters<- | Retrieve other_parameters from a result_model, result_collection, or musica object
other_parameters<--method | Retrieve other_parameters from a result_model, result_collection, or musica object

## -- P --

parameter | Retrieve parameter from a musica or result_collection object
parameter-method | Retrieve parameter from a musica or result_collection object
parameter<- | Retrieve parameter from a musica or result_collection object
parameter<--method | Retrieve parameter from a musica or result_collection 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_k_comparison | Plot k comparison
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

## -- R --

rc | Reverse complement of a string using biostrings
rep_range | Replication Timing Data as GRanges Object
res | res
result_collection-class | The Result Collection object that contains modality, input parameters, prior hyperparameters
result_list | Retrieve result_list from a musica object
result_list-method | Retrieve result_list from a musica object
result_list<- | Retrieve result_list from a musica object
result_list<--method | Retrieve result_list from a musica object
result_model-class | Object that contains results for a single model
res_annot | res_annot

## -- S --

sample_names | Retrieve sample names from a musica object
sample_names-method | Retrieve sample names from a musica object
samp_annot | Get or set sample annotations from a musica object
samp_annot-method | Get or set sample annotations from a musica object
samp_annot<- | Get or set sample annotations from a musica object
samp_annot<--method | Get or set sample annotations from a musica object
select_genome | Helper function to load common human or mouse genomes
signatures | Retrieve signatures from a result_model, result_collection, or musica object
signatures-method | Retrieve signatures from a result_model, result_collection, or musica object
signatures<- | Retrieve signatures from a result_model, result_collection, or musica object
signatures<--method | Retrieve signatures from a result_model, result_collection, or musica 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

## -- T --

tables | Retrieve the list of count_tables from a musica object
tables-method | Retrieve the list of count_tables from a musica object
tables<- | Retrieve the list of count_tables from a musica object
tables<--method | Retrieve the list of count_tables from a musica object
table_selected | Retrieve table name used for plotting from a result_model object
table_selected-method | Retrieve table name used for plotting from a result_model object

## -- U --

umap | Retrieve umap list from a result_model, result_collection, or musica object
umap-method | Retrieve umap list from a result_model, result_collection, or musica object
umap<- | Retrieve umap list from a result_model, result_collection, or musica object
umap<--method | Retrieve umap list from a result_model, result_collection, or musica object

## -- V --

variants | Retrieve variants from a musica object
variants-method | Retrieve variants from a musica object
variants<- | Retrieve variants from a musica object
variants<--method | Retrieve variants from a musica object