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

Documentation for package ‘mutSigExtractor’ version 1.14

DBS_SIGNATURE_PROFILES	DBS signature profiles
DBS_TYPES	Look up table for doublet base substitution types and reverse complement sequences
extractSigsDbs	Extract doublet substitution signatures
extractSigsIndel	Extract indel signatures
extractSigsSnv	Extract single nucleotide variant signatures
extractSigsSv	Extract structural variant signatures
fitToSignatures	Linear least-squares (non-negative) fitting
getContextsDbs	Extract doublet base substitution contexts
getContextsIndel	Extract indel sequence, type and length
getContextsSnv	Extract trinucleotide contexts
getContextsSv	Determine SV type and length
getInfoValues	Get values from INFO field
hello	Hello, World!
indelSeqFlanksStartEnd	Get the start/end positions for the left/right flanks of an indel
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
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)
splitDfRegex	Split data frame or matrix using regex on colnames
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.