CPsite_estimation       estimate the cpsites
CPsites                 predict the cleavage and polyadenylation(CP)
                        site
InPAS-package           alternative polyadenylation and cleavage
                        estimations
PAscore                 calculate the CP score
PAscore2                calculate the CP score
UTR3TotalCoverage       extract coverage of 3UTR for CP sites
                        prediction
UTR3eSet-class          Class 'UTR3eSet'
UTR3usage               calculate the usage of long and short form of
                        UTR3
covThreshold            calculate the cutoff threshold of coverage
coverageFromBedGraph    read coverage from bedGraph files
coverageRate            coverage rate of genes and 3UTRs
depthWeight             calculate the depth weight for each example
distalAdj               adjust distal CP sites by cleanUpdTSeq
filterRes               filter results
fisher.exact.test       do fisher exact test for two group datasets
get.regions.coverage    claculate coverage for giving region
getCov                  extract coverage from bedgraph file
getUTR3eSet             prepare dataset for test
getUTR3region           extract long and short 3UTR region
inPAS                   do estimation of alternative polyadenylation
                        and cleavage site in one step
lastCDSusage            extract coverage of last CDS exon region
limmaAnalyze            use limma to analyze the PDUI
optimalSegmentation     calculate SSE
polishCPs               polish the searching results of CP sites
prepare4GSEA            prepare the files for GSEA analysis
proximalAdj             adjust the proximal CP sites
proximalAdjByCleanUpdTSeq
                        adjust the proximal CP sites by cleanUpdTseq
proximalAdjByPWM        adjust the proximal CP sites by PWM
removeUTR3__UTR3        remove the candicates LIKE UTR3___UTR3
searchDistalCPs         search distal CP sites
searchProximalCPs       search proximal CPsites
seqLen                  get sequence lengths
singleGroupAnalyze      do analysis for single group samples
singleSampleAnalyze     do analysis for single sample
sortGR                  sort GRanges
testUsage               do test for dPDUI
totalCoverage           total coverage
trimSeqnames            trim the sequence names
usage4plot              prepare coverage data and fitting data for plot
utr3.hg19               3'UTR annotation for hg19 obtained from
                        utr3Annotation
utr3.mm10               3'UTR annotation for mm10 obtained from
                        utr3Annotation
utr3Annotation          extract 3'UTR from TxDb object
utr3UsageEstimation     estimation of 3'UTR usage for each region
valley                  get the local minimal square standard error
                        (SSE)
zScoreThrethold         calculate local background cutoff value
