Files in AlexJanse/cMut
Identify Clustered Single Nucleotide Mutations and Link Them to Mutational Patterns
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/createRandomMutations.R
R/createSummaryPatterns.R
R/dnaAlphabet.R
R/getClusterId.R
R/getSearchPatterns.R
R/getSummaryPatterns.R
R/groupClusters.R
R/identifyClusters.R
R/linkPatterns.R
R/mutationPatterns.R
R/searchClusterPatterns.R
R/shuffleMutations.R
R/sysdata.rda
R/testDataSet.R
README.md
cMut.Rproj
cran-comments.md
data/dnaAlphabet.rda
data/mutationPatterns.rda
data/testDataSet.rda
man/addClusterTableComment.Rd
man/addDistance.Rd
man/addIdentTableComment.Rd
man/addLinkPatterns.Rd
man/addShuffleMutationComment.Rd
man/callLinkPatterns.Rd
man/callSearchclusterPatterns.Rd
man/checkLinkPatternsParameters.Rd
man/checkParametersShuffleMutations.Rd
man/compare.Rd
man/compareContext.Rd
man/compareNucs.Rd
man/convertFactor.Rd
man/createGroupTable.Rd
man/createIdentTable.Rd
man/createRandomMutations.Rd
man/createRandomTable.Rd
man/createShuffleTable.Rd
man/createSummaryPatterns.Rd
man/dnaAlphabet.Rd
man/formatClusterMutations.Rd
man/fuseSurroundings.Rd
man/getAlphaMatches.Rd
man/getClusterId.Rd
man/getClusterType.Rd
man/getNnuc.Rd
man/getPatternIntersect.Rd
man/getRef.Rd
man/getRefData.Rd
man/getRevComTable.Rd
man/getReverseComplement.Rd
man/getSearchPatterns.Rd
man/getSummaryPatterns.Rd
man/groupClusters.Rd
man/identifyClusters.Rd
man/linkPatterns.Rd
man/mutationPatterns.Rd
man/nucToSymbol.Rd
man/searchClusterPatterns.Rd
man/setdiff.data.frame.Rd
man/shuffleMutations.Rd
man/shuffleParallel.Rd
man/summarizeBootstrap.Rd
man/testDataSet.Rd
tests/testthat.R
tests/testthat/extdata/randomData.txt
tests/testthat/extdata/shuffleTestResults.rds
tests/testthat/testCreateRandomMutations.R
tests/testthat/testGetSearchPatterns.R
tests/testthat/testGetSummaryPatterns.R
tests/testthat/testGroupClusters.R
tests/testthat/testIdentifyClusters.R
tests/testthat/testShuffleMutations.R
vignettes/ExamplePlotEnriched.png
vignettes/ExamplePlotNotEnriched.png
vignettes/analysis_of_clusterpatterns.Rmd
vignettes/firstTwoShuffleResults.rds
