proximalAdj: adjust the proximal CP sites

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

Description

adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq

Usage

proximalAdj(CPs, MINSIZE, PolyA_PWM, genome, classifier, classifier_cutoff, 
            shift_range, search_point_START, step=1)

Arguments

CPs	the outputs of searchProximalCPs
MINSIZE	min size for short from
PolyA_PWM	PolyA position weight metrix
genome	a BSgenome object
classifier	cleanUpdTSeq classifier
classifier_cutoff	cutoff value of the classiffier
shift_range	the searching range for the better CP sites
search_point_START	just in case there is no better CP sites
step	adjust step, default 1, means adjust by each base by cleanUpdTSeq.

Value

keep same as searchProximalCPs, which can be handled by polishCPs.

Author(s)

Jianhong Ou

See Also

searchProximalCPs, polishCPs, proximalAdjByPWM, proximalAdjByCleanUpdTSeq, PAscore,PAscore2

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.