Extracts SNV, indel, DBS, and SV signatures from vcf files.

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Documentation for package ‘mutSigExtractor’ version 1.29

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assignSigPerMut Assign a mutational signature to each mutation in a vcf or bed-like dataframe
cosSim Cosine similarity
cosSim.data.frame Cosine similarity
cosSim.default Cosine similarity
cosSim.matrix Cosine similarity
DBS_SIGNATURE_PROFILES DBS signature profiles
detSmnvType Determine SMNV type from REF and ALT
extractSigsDbs Extract doublet substitution signatures
extractSigsIndel Extract indel signatures
extractSigsIndelChord Extract indel signatures
extractSigsIndelPcawg Extract indel signatures
extractSigsSnv Extract single nucleotide variant signatures
extractSigsSv Extract structural variant signatures
fitToSignatures Linear least-squares (non-negative) fitting
fitToSignaturesFast Linear least-squares (non-negative) fitting
fitToSignaturesFastStrict Linear least-squares (non-negative) fitting
fitToSignaturesStrict Linear least-squares (non-negative) fitting
getContextsSv Determine SV type and length
getInfoValues Get values from INFO field
indelSeqFlanksStartEnd Get the start/end positions for the left/right flanks of an indel
INDEL_SIGNATURE_PROFILES Indel signature profiles
lsqnonneg Non-negative least squares fitting
lsqnonneg.data.frame Non-negative least squares fitting
lsqnonneg.default Non-negative least squares fitting
lsqnonneg.matrix Non-negative least squares fitting
nBasesMH Calculate the number of bases that are homologous to the 3' flanking sequence
nCopiesAlongFlank Calculate the number of copies of the indel sequence are present in the flank sequence
plotContexts Plot contexts
readSigsAsDf Read multiple files outputed my mutSigExtractor into a data frame
readVcfFields Read vcf into R as data frame
SBS_SIGNATURE_PROFILES_V2 SBS signature profiles (original 30)
SBS_SIGNATURE_PROFILES_V3 SBS signature profiles (new; v3, May 2019)
splitDfRegex Split data frame or matrix using regex on colnames
subsetSmnvs Subset for SNVs, DBSs, or indels
SV_SIGNATURE_PROFILES SV signature profiles
transformContexts Various transformation of contexts (e.g. into mutational signatures)
variantsFromVcf Extract relevant variant info for extracting SNV, indel, and SV signatures.