covThreshold


    coverage for each sample, 
        output of <a rd-options="" href="/link/coverageFromBedGraph?package=InPAS&version=1.4.4" data-mini-rdoc="InPAS::coverageFromBedGraph">coverageFromBedGraph</a>


coverage


    an object of <a rd-options="BSgenome" href="/link/BSgenome?package=InPAS&version=1.4.4&to=BSgenome" data-mini-rdoc="BSgenome::BSgenome">BSgenome</a>


genome


    an object of <a rd-options="GenomicFeatures" href="/link/TxDb?package=InPAS&version=1.4.4&to=GenomicFeatures" data-mini-rdoc="GenomicFeatures::TxDb">TxDb</a>


txdb


    output of <a rd-options="" href="/link/utr3Annotation?package=InPAS&version=1.4.4" data-mini-rdoc="InPAS::utr3Annotation">utr3Annotation</a>


utr3


    chromosome to be used for calculation, default is "chr1"



    is this dataset consume too much memory? 
        if it is TRUE, the coverage will be saved into tempfiles.


hugeData

groupList


    calculate the cutoff threshold of coverage for long form and short form


 misc 

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.

Jianhong Ou

InPAS

Identification of Novel alternative PolyAdenylation Sites (PAS)

covThreshold function


    coverage for each sample, 
        output of <a rd-options='' href='coverageFromBedGraph'>coverageFromBedGraph</a>



    an object of <a rd-options='BSgenome' href='BSgenome'>BSgenome</a>



    an object of <a rd-options='GenomicFeatures' href='TxDb'>TxDb</a>



    output of <a rd-options='' href='utr3Annotation'>utr3Annotation</a>


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covThreshold: calculate the cutoff threshold of coverage

Description

Usage

Arguments

Value

See Also