proximalAdj {InPAS}R Documentation

adjust the proximal CP sites

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


[Package InPAS version 1.16.0 Index]