# Somatic Signatures

## Documentation for package ‘SomaticSignatures’ version 2.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SomaticSignatures-package | SomaticSignatures package
assessNumberSignatures | Number of Signatures
cluster-spectrum | Cluster Mutational Spectrum
clusterSpectrum | Cluster Mutational Spectrum
decomposition-signatures | Decomposition Functions for Somatic Signatures
dfConvertColumns | Utility functions
findSignatures | Estimate Somatic Signatures
fitted | 'MutationalSignatures' class and methods
fitted-method | 'MutationalSignatures' class and methods
gcContent | GC Content
hs-chrs | Human Chromosome Names
hsAllosomes | Human Chromosome Names
hsAutosomes | Human Chromosome Names
hsLinear | Human Chromosome Names
hsToplevel | Human Chromosome Names
identifySignatures | Estimate Somatic Signatures
k3we | Kmer datasets
k3wg | Kmer datasets
kmerFrequency | Kmer Frequency
kmers | Kmer datasets
kmers-data | Kmer datasets
motifMatrix | Group somatic moticfs
mutational-normalization | Normalize Somatic Motifs
mutational-plots | Mutational Plots
mutational-signatures | Estimate Somatic Signatures
MutationalSignatures | 'MutationalSignatures' class and methods
MutationalSignatures-class | 'MutationalSignatures' class and methods
mutationContext | mutationContext functions
mutationContextMutect | mutationContext functions
mutationDistance | Distributions of mutational locations.
ncbi | GRanges converter functions
nmfDecomposition | Decomposition Functions for Somatic Signatures
nmfSignatures | Decomposition Functions for Somatic Signatures
normalizeMotifs | Normalize Somatic Motifs
observed | 'MutationalSignatures' class and methods
observed-method | 'MutationalSignatures' class and methods
pcaDecomposition | Decomposition Functions for Somatic Signatures
pcaSignatures | Decomposition Functions for Somatic Signatures
plotFittedSpectrum | Plot Mutational Signatures
plotMutationSpectrum | Plot Mutational Signatures
plotNumberSignatures | Number of Signatures
plotObservedSpectrum | Plot Mutational Signatures
plotRainfall | Distributions of mutational locations.
plotSampleMap | Plot Mutational Signatures
plotSamples | Plot Mutational Signatures
plotSignatureMap | Plot Mutational Signatures
plotSignatures | Plot Mutational Signatures
plotVariantAbundance | Mutational Plots
readMutect | readMutect
samples | 'MutationalSignatures' class and methods
samples-method | 'MutationalSignatures' class and methods
sca-data | SomaticCancerAlterations Results
sca_mm | SomaticCancerAlterations Results
sca_motifs_tiny | SomaticCancerAlterations Results
sca_sigs | SomaticCancerAlterations Results
seqchar | GRanges converter functions
show | 'MutationalSignatures' class and methods
show-method | 'MutationalSignatures' class and methods
signatures | 'MutationalSignatures' class and methods
signatures-method | 'MutationalSignatures' class and methods
signatures21 | 21 Signatures
signatures21-data | 21 Signatures
sigs_nmf | SomaticCancerAlterations Results
sigs_pca | SomaticCancerAlterations Results
SomaticSignatures | SomaticSignatures package
ucsc | GRanges converter functions
variants-utils | Utility functions