Files in friend1ws/pmsignature
Extracting characteristic mutation signatures from a set of mutation data.
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/DNPAnalysis.R
R/RcppExports.R
R/class.R
R/compareSignatures.R
R/getBackgroundProb.R
R/getSignature.R
R/mutationPositionPlot.R
R/mutationRatio.R
R/readFile.R
R/simulation.R
R/visualizeSignature.R
R/visualizeSignature2.R
README.html
README.md
inst/.DS_Store
inst/Todo
inst/bgdata/bg.full3.txt
inst/bgdata/bg.full3_dir.txt
inst/bgdata/bg.full5.txt
inst/bgdata/bg.full5_dir.txt
inst/bgdata/bg.full7.txt
inst/bgdata/bg.full7_dir.txt
inst/bgdata/bg.full9.txt
inst/bgdata/bg.full9_dir.txt
inst/bgdata/bg.ind3.txt
inst/bgdata/bg.ind3_dir.txt
inst/bgdata/bg.ind5.txt
inst/bgdata/bg.ind5_dir.txt
inst/bgdata/bg.ind7.txt
inst/bgdata/bg.ind7_dir.txt
inst/bgdata/bg.ind9.txt
inst/bgdata/bg.ind9_dir.txt
inst/extdata/.DS_Store
inst/extdata/Hoang_MFVF.full.txt.gz
inst/extdata/Hoang_MFVF.ind.txt.gz
inst/extdata/Nik_Zainal_2012.mutationPositionFormat.hg18.txt.gz
inst/extdata/Nik_Zainal_2012.mutationPositionFormat.txt.gz
inst/oldsrc/EMalgorithm.deprecated.cpp
inst/oldsrc/getSignature.deprecated.R
inst/oldsrc/readFile.R
inst/oldsrc/testFunction.R
inst/oldsrc/visualizeSignature.deprecated.R
inst/testSrc/EMalgorithm_test.cpp
inst/testSrc/getSignature_test.R
man/.Rapp.history
man/EstimatedParameters-class.Rd
man/MetaInformation-class.Rd
man/MutationFeatureData-class.Rd
man/PMSboundary.Rd
man/alignmentSignature.Rd
man/bootPMSignature.Rd
man/boundaryTurbo_F.Rd
man/boundaryTurbo_Q.Rd
man/calcPMSLikelihood.Rd
man/convertFromTurbo_F.Rd
man/convertFromTurbo_Q.Rd
man/convertSignatureMatrixToVector.Rd
man/convertToTurbo_F.Rd
man/convertToTurbo_Q.Rd
man/getBackgroudSignature.Rd
man/getCosDistance.Rd
man/getLogLikelihoodC.Rd
man/getMembershipValue.Rd
man/getMutMembership.Rd
man/getMutNum.Rd
man/getMutationFeatureVector.Rd
man/getPMSignature.Rd
man/getSignatureValue.Rd
man/getSignaturesForMultipleK.Rd
man/makeSimData.Rd
man/mySquareEM.Rd
man/readBGFile.Rd
man/readMFVFile.Rd
man/readMPFile.Rd
man/updateBackgroudSignatureFile.Rd
man/updateMstepFQC.Rd
man/updatePMSParam.Rd
man/updateTheta_NormalizedC.Rd
man/visMembership.Rd
man/visMembership2.Rd
man/visPMS_full.Rd
man/visPMS_ind.Rd
man/visPMSignature.Rd
pmsignature.Rproj
src/.gitignore
src/EMalgorithm.cpp
src/RcppExports.cpp
src/checkBoundary.cpp
src/convertFromToVector.cpp
tests/testthat.R
tests/testthat/test_mfv.R
tests/testthat/test_mp.R
vignettes/introduction.Rmd
vignettes/introduction.html
