Somatic Signatures


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Documentation for package ‘SomaticSignatures’ version 1.0.1

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SomaticSignatures-package SomaticSignatures package
dfConvertColumns Utility functions
extractSignatures Estimate Somatic Signatures
findSignatures Estimate Somatic Signatures
gcContent GC Content
grangesPlain GRanges converter functions
hs-chrs Human Chromosome Names
hsAllosomes Human Chromosome Names
hsAutosomes Human Chromosome Names
hsLinear Human Chromosome Names
hsToplevel Human Chromosome Names
k3we Kmer datasets
k3wg Kmer datasets
kmeansSignatures Estimate Somatic Signatures
kmerFrequency Kmer Frequency
kmers Kmer datasets
kmers-data Kmer datasets
mutational-normalization Normalize Somatic Motifs
mutational-plots Mutational Plots
mutational-signatures Estimate Somatic Signatures
mutationContext mutationContext functions
mutationContextH5vc mutationContext functions
mutationContextMatrix Estimate Somatic Signatures
mutationContextMutect mutationContext functions
mutationDistance Distributions of mutational locations.
ncbi GRanges converter functions
nmfSignatures Estimate Somatic Signatures
normalizeMotifs Normalize Somatic Motifs
pcaSignatures Estimate Somatic Signatures
plotRainfall Distributions of mutational locations.
plotSampleMap Estimate Somatic Signatures
plotSamples Estimate Somatic Signatures
plotSamplesObserved Estimate Somatic Signatures
plotSignatureMap Estimate Somatic Signatures
plotSignatures Estimate Somatic Signatures
plotVariantAbundance Mutational Plots
readMutect readMutect
seqchar GRanges converter functions
SomaticSignatures SomaticSignatures package
ucsc GRanges converter functions
variants-utils Utility functions