API for chrisamiller/copyCat
Find regions of genomic copy number loss and gain from short reads

Global functions
addBins Man page Man page Source code
addMapability Man page Source code
balancedCenter Man page Source code
binGC Man page Source code
binMap Man page Source code
binParams Man page
breakPointInt Man page Source code
cnNeutralDepthFromHetSites Man page Source code
cnSegments Man page Source code
cnSegments.paired Man page Source code
combineBins Man page Source code
combinePercBins Man page Source code
coverageFilter Man page
doCorrection Man page Source code
doSegPlot Man page Source code
dumpParams Man page Source code
gcCorrect Man page Source code
getAlts Man page Source code
getAnnoDir Man page Source code
getChrLength Man page Source code
getChrPloidy Man page Source code
getMedianReadCount Man page Source code
getNumReads Man page Source code Source code
getReadDepth Man page Source code
getSegs Man page Source code
getWindowBins Man page Source code
inferSamtoolsFormat Source code
initRdClass Man page Source code
listify Man page Source code
loessCorrect Man page Source code
logScore Man page Source code
makeCorrBins Man page Source code
makeCorrBinsMedian Man page Source code
makeDf Man page Source code
makeDfLog Man page Source code
makeDfLogPaired Man page Source code
makeDfPaired Man page Source code
makeMapDf Man page Source code
mapCorrect Man page Source code
mergeLibraries Man page Source code
mergeSegs Man page Source code
methAdjust Man page Source code
onLoad Source code
parseSamtools10col Source code
parseSamtoolsVcf Source code
ploidyPercentages Man page
plotGcLoess Man page Source code
plotMapLoess Man page Source code
plotSegs Man page Source code
plotSegsPaired Man page Source code
plotSegsPairedLog Man page Source code
plotWindows Man page Source code
rdObject-class Man page
readEntrypoints Man page Source code
refineBreakpoints Man page Source code
removeCoverageArtifacts Man page Source code
removeGapCounts Man page
removeGapSpanningSegments Man page Source code
replaceReadCounts Man page Source code
returnOutliers Man page Source code
rpois.od Man page Source code
runPairedSampleAnalysis Man page Source code
runSingleSampleAnalysis Man page Source code
setParams Man page Source code
stripOutliers Man page Source code
subsetByReadLength Man page Source code
subtractBins Man page Source code
trimSegmentEnds Man page Source code
writeAlts Man page Source code
writeBins Man page Source code
writePairedBins Man page Source code
writeSegs Man page Source code
writeThresholds Man page Source code
chrisamiller/copyCat documentation built on Dec. 2, 2017, 4:28 a.m.