addSegDat | addSegDat |
affy.omni | Mapping of Omni 2.5M probesets to Affy SNP6.0 |
annoDemoMat | annoDemoMat |
annotateSegments | cnTools: annotate GRanges segments |
assemblePredDat | assemblePredDat |
assignGrpIDs | pIDs |
availableRefCCL | availableRefCCL |
bafDrift | bafDrift |
balanceGrps | balanceGrps |
ccl_table | Table containing links to external datasets and BAF matrices |
checkAgainst | checkAgainst |
checkForConcordance | checkForConcordance |
checkMse | checkMse |
cin70 | Chromosomal instability (CIN) 70 genes from... |
combineSamples | combineSamples |
compareVcf | compareVcf |
corWithDrug | corWithDrug |
demoSample | demoSample |
dot-addCumPos | .addCumPos |
dot-addSegSd | addSegSd |
dot-blankGr | .blankGr |
dot-chkAndDownload | Check and download |
dot-compSegs | .compSegs |
dot-demo | Demo |
dot-demoDeconvolution | Title |
dot-estimateDrift | .estimateDrift |
dot-estimateZcutoff | .estimateZcutoff |
dot-filt | .filt |
dot-fixGT | .fixGT |
dot-genMatchSnpDiff | .genMatchSnpDiff |
dot-genNonmatchSnpDiff | .genNonmatchSnpDiff |
dot-getChrLength | .getChrLength |
dot-getDerivedFrom | .getDerivedFrom |
dot-getDrift | .getDrift |
dot-getSynonymous | .getSynonymous |
dot-getVariantFeatures | .getVariantFeatures |
dot-grepNA | .grepNA |
dot-jsonToGr | .jsonToGr |
dot-meltDf | Melts dataframe |
dot-normBAF | .normBAF |
dot-overlapProbeset | .overlapProbeset |
dot-revComp | .revComp |
dot-vcf2AffyGT | .vcf2AffyGT |
dot-zval | z-statistic |
downloadRefCCL | downloadRefCCL |
driftOverlap | driftOverlap |
driftOverlapMetric | driftOverlapMetric |
findCclPairs | findCclPairs |
formatRefMat | formatRefMat |
fullpull | fullpull |
genDemoData | genDemoData |
genErrBp | genErrBp |
getBafDrifts | getBafDrifts |
getCinScore | getCinScore |
getCNDrifts | getCnDrifts |
getCVCL | getCVCL |
getGeneExpr | getGeneExpr |
getGenes | cnTools: get Genes in TxDb.Hsapiens.UCSC.hg19.knownGene |
getSegSD | get Seg SD |
getVcfDrifts | getVcfDrifts |
gne.meta | Metadata for gCSI dataset |
loadInPSets | loadInPSets |
loadRef | loadRef |
mapVariantFeat | mapVariantFeat |
mapVcf2Affy | mapVcf2Affy |
meta.df | Metadata mapping together all pharmacogenomic datasets and... |
mkPredictions | mkPredictions |
multiDriftPlot | multiDriftPlot OUTDATED |
overlapPos | overlapPos |
plot.CCLid | plot.CCLid plot() function for CCLid adjusted DNAcopy segment... |
plotFracDrift | plotFracDrift |
plotHist | plotHist |
plot.multiObj | plot.multiObj |
plot.SimpleCCLid | plot.SimpleCCLid |
readinRnaFileMapping | readinRnaFileMapping |
rna.meta.df | Metadata mapping together all pharmacogenomic datasets and... |
segmentDrift | segmentDrift |
sigDiffBaf | sigDiffBaf |
similarityMatrix | similarityMatrix |
snp6.dat | BED file of SNP6 Probeset IDs and genomic loci in hg19 |
splitConcordanceVals | splitConcordanceVals |
splitToMNM | splitToMNM |
summarizeFracDrift | summarizeFracDrift |
trainLogit | trainLogit |
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