Man pages for raerose01/deconstructSigs
Identifies Signatures Present in a Tumor Sample

changeColumnNamesRe-formats column names
dbs_possibleTable of Possible DBS mutations and their reverse complement
deconstructSigsdeconstructSigs
example.outputExample output of whichSignatures()
findSeedSeeds weight matrix
formatContextsFormats the data for use in plotSignatures()
getErrorCalculates error
getTriContextFractionCalculates trinucleotide context fraction
golden.section.searchGolden section search
makePiePlots the weights from whichSignatures()
mut.to.sigs.inputConverts mutation list to correct input format
norm.itNormalizes trinucleotide contexts
plotSignaturesPlots the result from whichSignatures()
plotTumorPlots a tumor profile
randomly.generated.tumorsValues for 100 randomly generated tumor samples
sample.mut.refExample input to mut.to.sigs.input()
signatures.cosmicPublished Signatures from Sanger COSMIC
signatures.dbs.cosmic.v3.may2019New DBS Signatures from Sanger COSMIC (May 2019)
signatures.exome.cosmic.v3.may2019Updated SBS Exome Signatures from Sanger COSMIC (May 2019)
signatures.genome.cosmic.v3.may2019Updated SBS Genome Signatures from Sanger COSMIC (May 2019)
signatures.nature2013Published Signatures from Alexandrov et al 2013
tri.counts.exomeThe counts of every trinuclotide frequency in an exome
tri.counts.genomeThe counts of every trinuclotide frequency in a genome
updateW_GRUpdates the weights matrix
vcf.to.sigs.inputConverts a VCF file to correct input format
whichSignaturesWhich signatures are present
raerose01/deconstructSigs documentation built on Oct. 16, 2019, 6:23 p.m.