Comprehensive genome-wide analysis of mutational processes

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Documentation for package ‘MutationalPatterns’ version 1.4.1

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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