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InPAS (version 1.4.4)

Identification of Novel alternative PolyAdenylation Sites (PAS)

Description

Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.

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Version

Version

1.4.4

License

GPL (>= 2)

Maintainer

Jianhong Ou

Last Published

February 15th, 2017

Functions in InPAS (1.4.4)

filterRes

filter results
CPsite_estimation

estimate the cpsites
optimalSegmentation

calculate SSE
CPsites

predict the cleavage and polyadenylation(CP) site
fisher.exact.test

do fisher exact test for two group datasets
InPAS-package

alternative polyadenylation and cleavage estimations
inPAS

do estimation of alternative polyadenylation and cleavage site in one step
singleGroupAnalyze

do analysis for single group samples
singleSampleAnalyze

do analysis for single sample
sortGR

sort GRanges
testUsage

do test for dPDUI
valley

get the local minimal square standard error (SSE)
zScoreThrethold

calculate local background cutoff value
PAscore

calculate the CP score
seqLen

get sequence lengths
searchProximalCPs

search proximal CPsites
usage4plot

prepare coverage data and fitting data for plot
utr3.hg19

3'UTR annotation for hg19 obtained from utr3Annotation
depthWeight

calculate the depth weight for each example
distalAdj

adjust distal CP sites by cleanUpdTSeq
proximalAdjByCleanUpdTSeq

adjust the proximal CP sites by cleanUpdTseq
proximalAdjByPWM

adjust the proximal CP sites by PWM
trimSeqnames

trim the sequence names
totalCoverage

total coverage
lastCDSusage

extract coverage of last CDS exon region
limmaAnalyze

use limma to analyze the PDUI
utr3.mm10

3'UTR annotation for mm10 obtained from utr3Annotation
prepare4GSEA

prepare the files for GSEA analysis
utr3Annotation

extract 3'UTR from TxDb object
proximalAdj

adjust the proximal CP sites
get.regions.coverage

claculate coverage for giving region
getCov

extract coverage from bedgraph file
getUTR3eSet

prepare dataset for test
removeUTR3__UTR3

remove the candicates LIKE UTR3___UTR3
getUTR3region

extract long and short 3UTR region
searchDistalCPs

search distal CP sites
UTR3eSet-class

Class UTR3eSet
UTR3TotalCoverage

extract coverage of 3UTR for CP sites prediction
coverageFromBedGraph

read coverage from bedGraph files
covThreshold

calculate the cutoff threshold of coverage
PAscore2

calculate the CP score
polishCPs

polish the searching results of CP sites
UTR3usage

calculate the usage of long and short form of UTR3
utr3UsageEstimation

estimation of 3'UTR usage for each region