Rd file 'BayesCptCI.Rd':
  \usage lines wider than 90 characters:
     BayesCptCI(cases, controls, CBSRes, stepSize="adaptive", adaptMaxMix=80, alpha=0.05, epsilon=10^-4, epsCDF=10^-4, verbose=FALSE)

Rd file 'CombineReadsAcrossRuns.Rd':
  \examples lines wider than 100 characters:
     write.table(JSSim_NormalSim1, file="JSSim_NormalSim1.txt", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
     write.table(JSSim_NormalSim2, file="JSSim_NormalSim2.txt", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)

Rd file 'ScanCBS.Rd':
  \usage lines wider than 90 characters:
     ScanCBS(cases, controls, statistic = "binomial", grid.size = "auto", takeN = 5, maxNCut = 100, minStat = 0, alpha=0.05, verbose = FALSE ... [TRUNCATED]

Rd file 'ScanCBSPlot.Rd':
  \usage lines wider than 90 characters:
     ScanCBSPlot(cases, controls, CBSObj, filename, mainTitle, CIObj=NULL, length.out=10000, localWindow=0.5*10^5, localSeparatePlot=TRUE, s ... [TRUNCATED]

Rd file 'ScanCBSSimPlot.Rd':
  \usage lines wider than 90 characters:
     ScanCBSSimPlot(cases, controls, CBSObj, trueTau, SpikeMat, filename, mainTitle, CIObj=NULL, length.out=10000, localWindow=0.5*10^5, loc ... [TRUNCATED]

Rd file 'ScanIterateGrid.Rd':
  \usage lines wider than 90 characters:
     ScanIterateGrid(combX, combZ, combL, statistic, grid.size, nGridSize, timeIGSBreakDown, takeN, verbose, timing)

Rd file 'ScanStatNewComp.Rd':
  \usage lines wider than 90 characters:
     ScanStatNewComp(combZCumSum, combXCumSum, combZPoint, combXPoint, p, nTotal, grid.cur, max.win, statistic)

Rd file 'ScanStatRefineComp.Rd':
  \usage lines wider than 90 characters:
     ScanStatRefineComp(combZCumSum, combXCumSum, combZPoint, combXPoint, p, nTotal, grid.cur, grid.LR, max.win, statistic)

Rd file 'nhppSimConstWindowAnalysis.Rd':
  \usage lines wider than 90 characters:
     nhppSimConstWindowAnalysis(filePrefix, chromosomeN, distMetric=c(20,50,100,150,200,300,500,1000), cptLen=c(3,5,8,12,15,20,30,50,100), n ... [TRUNCATED]

Rd file 'nhppSimConstWindowGen.Rd':
  \usage lines wider than 90 characters:
     nhppSimConstWindowGen(controlRates, filename, chromosomeN, nSpike=25, cptLen=c(3,5,8,12,20,30,50,75,100), nPair=2, nRepeat=10, minGain= ... [TRUNCATED]

Rd file 'nhppSpike.Rd':
  \usage lines wider than 90 characters:
     nhppSpike(smoothRates, nSpike = 25, cptLenR = 4, cptLenMean = 10, minGain = 1.5, maxGain = 10, minLoss = 0.01, maxLoss = 0.5, pGain = 0 ... [TRUNCATED]

Rd file 'nhppSpikeConstWindow.Rd':
  \usage lines wider than 90 characters:
     nhppSpikeConstWindow(smoothRates, nSpike = 25, cptLen = 5, minGain = 1.5, maxGain = 10, minLoss = 0.01, maxLoss = 0.5, pGain = 0.6)

These lines will be truncated in the PDF manual.