# Comprehensive genome-wide analysis of mutational processes

## Documentation for package ‘MutationalPatterns’ version 2.0.0

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

## Help Pages

MutationalPatterns-package | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
binomial_test | Binomial test for enrichment or depletion testing
cluster_signatures | Signature clustering function
cos_sim | Cosine similarity function
cos_sim_matrix | Compute all pairwise cosine similarities between mutational profiles/signatures
enrichment_depletion_test | Test for enrichment or depletion of mutations in genomic regions
explained_by_signatures | This function has been renamed to 'cos_sim_matrix'.
extract_signatures | Extract mutational signatures from 96 mutation matrix using NMF
fit_to_signatures | Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.
genomic_distribution | Find overlaps between mutations and a genomic region.
MutationalPatterns | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
mutations_from_vcf | Retrieve base substitutions from vcf
mutation_context | This function has been removed. Use 'mut_context' instead.
mutation_types | This function has been renamed. Use 'mut_type' instead.
mut_context | Retrieve context of base substitutions
mut_matrix | Make mutation count matrix of 96 trinucleotides
mut_matrix_stranded | Make mutation count matrix of 96 trinucleotides with strand information
mut_strand | Find strand of mutations
mut_type | Retrieve base substitution types from a VCF object
mut_type_occurrences | Count the occurrences of each base substitution type
plot_192_profile | Plot 192 trinucleotide profile
plot_96_profile | Plot 96 trinucleotide profile
plot_compare_profiles | Compare two 96 mutation profiles
plot_contribution | Plot signature contribution barplot
plot_contribution_heatmap | Plot signature contribution heatmap
plot_cosine_heatmap | Plot cosine similarity heatmap
plot_enrichment_depletion | Plot enrichment/depletion of mutations in genomic regions
plot_rainfall | Plot genomic rainfall
plot_signature_strand_bias | Plot signature strand bias
plot_spectrum | Plot point mutation spectrum
plot_strand | Plot strand per base substitution type
plot_strand_bias | Plot strand bias per base substitution type per group
read_vcfs_as_granges | Read VCF files into a GRangesList
strand_bias_test | Significance test for strand asymmetry
strand_from_vcf | This function has been renamed. Use 'mut_strand' instead.
strand_occurrences | Count occurrences per base substitution type and strand
type_context | Retrieve context of base substitution types