Mutational Signature Comprehensive Analysis Toolkit

Documentation for package ‘musicatk’ version 2.0.0

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-- A --

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

-- 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_result_model	Load an external model into a result_model object
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

-- 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-method	Retrieve model_id 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