Files in rmpiro/decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refitting
DESCRIPTION
NAMESPACE
R/QPforSig.R
R/addBestSignatureToSubset.R
R/adjustSignaturesForRegionSet.R
R/buildGenomesFromMutationData.R
R/buildSortedAlexandrovSignaturePatternList.R
R/composeGenomesFromExposures.R
R/computeExplainedVariance.R
R/convAlx2Shi.R
R/convertAlexandrov2Shiraishi.R
R/convertGenomesFromVRanges.R
R/decompTumor2Sig-package.R
R/decomposeTumorGenomes.R
R/determineSignatureDistances.R
R/determineTypeNumBasesAndTrDir.R
R/downgradeShiraishiSignatures.R
R/evaluateDecompositionQuality.R
R/external_classes_wrapper_functions.R
R/getBestDecomp4Ksignatures.R
R/getGenomesFromMutFeatData.R
R/getSignaturesFromEstParam.R
R/helper_functions_for_class_checks.R
R/helper_functions_for_sequences.R
R/mapSignatureSets.R
R/mathematical_functions.R
R/onAttach.R
R/plotAlexandrovModel.R
R/plotDecomposedContribution.R
R/plotExplainedVariance.R
R/plotMutationDistribution.R
R/plotShiraishiModel.R
R/processMultipleSigSets.R
R/readAlexandrovSignatures.R
R/readGenomesFromMPF.R
R/readGenomesFromVCF.R
R/readShiraishiSignatures.R
R/setNames4ShiraishiTable.R
README.md
decompTumor2Sig-manual.pdf
inst/CITATION
inst/NEWS
inst/extdata/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.Rdata
inst/extdata/Nik-Zainal_PMID_22608084-MPF.txt.gz
inst/extdata/Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz
inst/extdata/Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata
inst/extdata/Nik-Zainal_PMID_22608084-genomes-Shiraishi_5bases_trDir.Rdata
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-G.Rdata
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-Param.Rdata
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig1.tsv
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig2.tsv
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig3.tsv
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig4.tsv
inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sigall.Rdata
inst/license/COPYING
inst/script/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.R
inst/script/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.sh
inst/script/Nik-Zainal_PMID_22608084-MPF.txt.gz.sh
inst/script/Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz.sh
inst/script/Nik-Zainal_PMID_22608084-genomes.R
inst/script/Nik-Zainal_PMID_22608084-pmsignature.R
inst/script/extractSpecColumns.pl
inst/script/filterLines.pl
inst/script/filterLinesNumeric.pl
man/QPforSig.Rd
man/addBestSignatureToSubset.Rd
man/adjustAlexandrovSignature.Rd
man/adjustShiraishiSignature.Rd
man/adjustSignaturesForRegionSet.Rd
man/buildGenomesFromMutationData.Rd
man/buildSortedAlexandrovSignaturePatternList.Rd
man/compNucFreq.Rd
man/composeGenomesFromExposures.Rd
man/computeExplainedVariance.Rd
man/computeFrobeniusNorm.Rd
man/computeRSS.Rd
man/convAlx2Shi.Rd
man/convertAlexandrov2Shiraishi.Rd
man/convertGenomesFromVRanges.Rd
man/convertSeqFreqToBaseFreq.Rd
man/decompTumor2Sig-package.Rd
man/decomposeTumorGenomes.Rd
man/determineSignatureDistances.Rd
man/determineTypeNumBasesAndTrDir.Rd
man/downgradeShiraishiSignatures.Rd
man/evaluateDecompositionQuality.Rd
man/getBestDecomp4Ksignatures.Rd
man/getCountData.Rd
man/getFeatVectList.Rd
man/getGenomesFromMutFeatData.Rd
man/getNumFlankingBases.Rd
man/getNumSignatures.Rd
man/getSampleList.Rd
man/getSigFeatDist.Rd
man/getSigFromEstParam.Rd
man/getSigType.Rd
man/getSignaturesFromEstParam.Rd
man/haveTrDir.Rd
man/is.probability.data.frame.Rd
man/is.probability.data.frame.list.Rd
man/is.probability.matrix.Rd
man/is.probability.matrix.list.Rd
man/is.probability.object.Rd
man/is.probability.vector.Rd
man/is.probability.vector.list.Rd
man/isAlexandrovSet.Rd
man/isBackGround.Rd
man/isEstParamObject.Rd
man/isExposureSet.Rd
man/isMutFeatDataObject.Rd
man/isShiraishiSet.Rd
man/isSignatureSet.Rd
man/mapSignatureSets.Rd
man/plotAlexandrovModel.Rd
man/plotDecomposedContribution.Rd
man/plotExplainedVariance.Rd
man/plotMutationDistribution.Rd
man/plotShiraishiModel.Rd
man/processMultipleSigSets.Rd
man/readAlexandrovSignatures.Rd
man/readGenomesFromMPF.Rd
man/readGenomesFromVCF.Rd
man/readShiraishiSignatures.Rd
man/roundIntegerSum.Rd
man/sameSignatureFormat.Rd
man/setNames4ShiraishiTable.Rd
man/setNumFlankingBases.Rd
man/setSigFeatDist.Rd
man/setSigType.Rd
man/setTrDir.Rd
vignettes/decompTumor2Sig.Rmd
vignettes/example-sign-Shiraishi.png
