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

## Documentation for package ‘mutSigExtractor’ version 2.1.0

- DESCRIPTION file.

## Help Pages

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.