Mutational Signature Comprehensive Analysis Toolkit

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Documentation for package ‘musicatk’ version 1.15.1

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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
musicatk Starts the musicatk interactive Shiny app
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