Studying patterns in base substitution catalogues

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Documentation for package ‘MutationalPatterns’ version 0.2

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MutationalPatterns-package MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
bed_to_granges Read bed files as a list of GRanges objects
binomial_test Binomial test for enrichment or depletion testing
enrichment_depletion_test Test for enrichment or depletion of mutations in genomic regions
estimate_rank Estimate optimal rank for NMF decomposition
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
get_muts Retrieve base substitutions from vcf
get_mut_context Retrieve context of base substitutions
get_strand Find transcriptional strand of base substitutions in vcf
get_types Retrieve base substitution types from vcf
get_type_context Retrieve context of base substitution types
intersect_with_region Find overlap between mutations and a genomic region
MutationalPatterns MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
mut_192_occurences Count 96 trinucleotide mutation occurences with transcriptional strand information
mut_96_occurences Count 96 trinucleotide mutation occurences
mut_matrix Make mutation count matrix of 96 trinucleotides
mut_matrix_stranded Make mutation count matrix of 96 trinucleotides with transcriptional strand information
mut_type_occurences Count the occurences of each base substitution type
plot_192_profile Plot 192 trinucleotide profile Plot relative contribution of 192 trinucleotides
plot_96_profile Plot 96 trinucleotide profile Plot relative contribution of 96 trinucleotides
plot_compare_profiles Compare two 96 mutation profiles
plot_contribution Plot signature contribution
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
read_vcf Read vcf files into list of CollapsedVCF objects
rename_chrom Rename chromosome names to standard
strand_bias_test Significance test for transcriptional strand asymmetry
strand_occurences Count occurences per base substitution type and transcriptional strand