Somatic Signatures


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Documentation for package ‘SomaticSignatures’ version 2.2.3

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SomaticSignatures-package SomaticSignatures package
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
mutationContextH5vc 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
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
scaSNVRanges SNV VRanges from SCA dataset
sca_mm 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