Man pages for CuppenResearch/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes

binomial_testBinomial test for enrichment or depletion testing
cluster_signaturesSignature clustering function
cos_simCosine similarity function
cos_sim_matrixCompute all pairwise cosine similarities between mutational...
enrichment_depletion_testTest for enrichment or depletion of mutations in genomic...
explained_by_signaturesThis function has been renamed to 'cos_sim_matrix'.
extract_signaturesExtract mutational signatures from 96 mutation matrix using...
fit_to_signaturesFind optimal nonnegative linear combination of mutation...
genomic_distributionFind overlaps between mutations and a genomic region.
MutationalPatterns-packageMutationalPatterns: an integrative R package for studying...
mutation_contextThis function has been removed. Use 'mut_context' instead.
mutations_from_vcfRetrieve base substitutions from vcf
mutation_typesThis function has been renamed. Use 'mut_type' instead.
mut_contextRetrieve context of base substitutions
mut_matrixMake mutation count matrix of 96 trinucleotides
mut_matrix_strandedMake mutation count matrix of 96 trinucleotides with strand...
mut_strandFind strand of mutations
mut_typeRetrieve base substitution types from a VCF object
mut_type_occurrencesCount the occurrences of each base substitution type
plot_192_profilePlot 192 trinucleotide profile
plot_96_profilePlot 96 trinucleotide profile
plot_compare_profilesCompare two 96 mutation profiles
plot_contributionPlot signature contribution barplot
plot_contribution_heatmapPlot signature contribution heatmap
plot_cosine_heatmapPlot cosine similarity heatmap
plot_enrichment_depletionPlot enrichment/depletion of mutations in genomic regions
plot_rainfallPlot genomic rainfall
plot_signature_strand_biasPlot signature strand bias
plot_spectrumPlot point mutation spectrum
plot_strandPlot strand per base substitution type
plot_strand_biasPlot strand bias per base substitution type per group
read_vcfs_as_grangesRead VCF files into a GRangesList
strand_bias_testSignificance test for strand asymmetry
strand_from_vcfThis function has been renamed. Use 'mut_strand' instead.
strand_occurrencesCount occurrences per base substitution type and strand
type_contextRetrieve context of base substitution types
CuppenResearch/MutationalPatterns documentation built on Dec. 19, 2017, 4:01 p.m.