proximalAdj


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


MINSIZE

PolyA_PWM


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


genome

classifier

classifier_cutoff


    the searching range for the better CP sites


shift_range


    just in case there is no better CP sites


search_point_START


    adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq


 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)

proximalAdj function


    the outputs of <a rd-options='' href='searchProximalCPs'>searchProximalCPs</a>



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


proximalAdj: adjust the proximal CP sites

Description

Usage

Arguments

Value

See Also