# InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

## Documentation for package ‘InPAS’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

InPAS-package | alternative polyadenylation and cleavage estimations
$-method | Class 'UTR3eSet'
$<--method | Class 'UTR3eSet'
coverageFromBedGraph | read coverage from bedGraph files
coverageRate | coverage rate of genes and 3UTRs
covThreshold | calculate the cutoff threshold of coverage
CPsites | predict the cleavage and polyadenylation(CP) site
CPsite_estimation | estimate the cpsites
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 | alternative polyadenylation and cleavage estimations
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
PAscore | calculate the CP score
PAscore2 | calculate the CP score
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.danRer10 | 3'UTR annotation for danRer10 obtained from utr3Annotation
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
UTR3eSet | Class 'UTR3eSet'
UTR3eSet-class | Class 'UTR3eSet'
UTR3TotalCoverage | extract coverage of 3UTR for CP sites prediction
UTR3usage | calculate the usage of long and short form of UTR3
utr3UsageEstimation | estimation of 3'UTR usage for each region
valley | get the local minimal square standard error (SSE)
zScoreThrethold | calculate local background cutoff value