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

bin_mutation_densityBin the genome based on mutation density
binomial_testBinomial test for enrichment or depletion testing
calculate_lesion_segregationCalculate the amount of lesion segregation for a GRangesList...
cluster_signaturesSignature clustering function
context_potential_damage_analysisPotential damage analysis for the supplied mutational...
convert_sigs_to_refConvert tissue specific signature exposures to reference
cos_simCosine similarity function
cos_sim_matrixCompute all pairwise cosine similarities between mutational...
count_dbs_contextsCount DBS contexts
count_indel_contextsCount indel contexts
count_mbs_contextsCount MBS variants grouped by length.
determine_regional_similarityDetermine regional mutation pattern similarity
enrichment_depletion_testTest for enrichment or depletion of mutations in genomic...
extract_signaturesExtract mutational signatures from 96 mutation matrix using...
fit_to_signaturesFind optimal nonnegative linear combination of mutation...
fit_to_signatures_bootstrappedFit mutational signatures to a mutation matrix with...
fit_to_signatures_strictFit mutational signatures to a mutation matrix with less...
genomic_distributionFind overlaps between mutations and a genomic region.
get_dbs_contextGet DBS context
get_indel_contextGet indel contexts
get_known_signaturesGet known signatures
get_mut_typeGet variants with mut_type from GRanges
get_sim_tbAn S4 generic to get the sim_tb from a region_cossim object.
lengthen_mut_matrixLengthen mutation matrix
merge_signaturesMerge signatures based on cosine similarity
mut_192_occurrencesCount 192 trinucleotide mutation occurrences
mut_96_occurrencesCount 96 trinucleotide mutation occurrences
MutationalPatterns-defunctDefunct functions in package 'MutationalPattern'
MutationalPatterns-packageMutationalPatterns: an integrative R package for studying...
mutations_from_vcfRetrieve base substitutions from vcf
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_bootstrapped_contributionPlot the bootstrapped signature contributions
plot_compare_dbsCompare two DBS mutation profiles
plot_compare_indelsCompare two indel mutation profiles
plot_compare_mbsCompare two mbs mutation profiles
plot_compare_profilesCompare two 96 mutation profiles
plot_contributionPlot signature contribution barplot
plot_contribution_heatmapPlot signature contribution heatmap
plot_correlation_bootstrapPlots the correlation between bootstrapped signature...
plot_cosine_heatmapPlot cosine similarity heatmap
plot_dbs_contextsPlot the DBS contexts
plot_enrichment_depletionPlot enrichment/depletion of mutations in genomic regions
plot_indel_contextsPlot the indel contexts
plot_lesion_segregationPlot the strands of variants to show lesion segregation
plot_main_dbs_contextsPlot the main DBS contexts
plot_main_indel_contextsPlot the main indel contexts
plot_mbs_contextsPlot the MBS contexts
plot_original_vs_reconstructedPlot the similarity between a mutation matrix and its...
plot_profile_heatmapPlot a mutation matrix as a heatmap
plot_profile_regionPlot 96 trinucleotide profile per subgroup
plot_rainfallPlot genomic rainfall
plot_regional_similarityPlot regional similarity
plot_riverPlot a riverplot
plot_signature_strand_biasPlot signature strand bias
plot_spectrumPlot point mutation spectrum
plot_spectrum_regionPlot point mutation spectrum per genomic region
plot_strandPlot strand per base substitution type
plot_strand_biasPlot strand bias per base substitution type per group
pool_mut_matPool multiple samples from a mutation matrix together
read_vcfs_as_grangesRead VCF files into a GRangesList
region_cossim-classAn S4 class to store the results of a regional mutation...
rename_nmf_signaturesRename NMF signatures based on previously defined signatures
show-region_cossim-methodAn S4 method to show an instance of the region_cossim class.
signature_potential_damage_analysisPotential damage analysis for the supplied mutational...
split_muts_regionSplit GRangesList or GRanges based on a list of regions.
strand_bias_testSignificance test for strand asymmetry
strand_occurrencesCount occurrences per base substitution type and strand
type_contextRetrieve context of base substitution types
CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.