Man pages for jianhong/InPAS
Identification of Novel alternative PolyAdenylation Sites (PAS)

coverageFromBedGraphread coverage from bedGraph files
coverageRatecoverage rate of genes and 3UTRs
covThresholdcalculate the cutoff threshold of coverage
CPsite_estimationestimate the cpsites
CPsitespredict the cleavage and polyadenylation(CP) site
depthWeightcalculate the depth weight for each example
distalAdjadjust distal CP sites by cleanUpdTSeq
filterResfilter results
fisher.exact.testdo fisher exact test for two group datasets
getCovextract coverage from bedgraph file
get.regions.coverageclaculate coverage for giving region
getUTR3eSetprepare dataset for test
getUTR3regionextract long and short 3UTR region
inPASdo estimation of alternative polyadenylation and cleavage...
InPAS-packagealternative polyadenylation and cleavage estimations
lastCDSusageextract coverage of last CDS exon region
limmaAnalyzeuse limma to analyze the PDUI
optimalSegmentationcalculate SSE
PAscorecalculate the CP score
PAscore2calculate the CP score
polishCPspolish the searching results of CP sites
prepare4GSEAprepare the files for GSEA analysis
proximalAdjadjust the proximal CP sites
proximalAdjByCleanUpdTSeqadjust the proximal CP sites by cleanUpdTseq
proximalAdjByPWMadjust the proximal CP sites by PWM
removeUTR3__UTR3remove the candicates LIKE UTR3___UTR3
searchDistalCPssearch distal CP sites
searchProximalCPssearch proximal CPsites
seqLenget sequence lengths
singleGroupAnalyzedo analysis for single group samples
singleSampleAnalyzedo analysis for single sample
sortGRsort GRanges
testUsagedo test for dPDUI
totalCoveragetotal coverage
trimSeqnamestrim the sequence names
usage4plotprepare coverage data and fitting data for plot
utr3Annotationextract 3'UTR from TxDb object
utr3.danRer103'UTR annotation for danRer10 obtained from utr3Annotation
UTR3eSetClass 'UTR3eSet'
utr3.hg193'UTR annotation for hg19 obtained from utr3Annotation
utr3.mm103'UTR annotation for mm10 obtained from utr3Annotation
UTR3TotalCoverageextract coverage of 3UTR for CP sites prediction
UTR3usagecalculate the usage of long and short form of UTR3
utr3UsageEstimationestimation of 3'UTR usage for each region
valleyget the local minimal square standard error (SSE)
zScoreThretholdcalculate local background cutoff value
jianhong/InPAS documentation built on Nov. 3, 2018, 9:08 a.m.