proximalAdjByPWM {InPAS}R Documentation

adjust the proximal CP sites by PWM

Description

adjust the proximal CP sites by polyA Position Weight Metrix. It only need the PWM get match in upstream or downstream shift_range nr.

Usage

proximalAdjByPWM(idx, PolyA_PWM, seqnames, starts, strands, genome, 
                 shift_range, search_point_START)

Arguments

idx

the offset of positions of CP sites

PolyA_PWM

polyA PWM

seqnames

sequence names

starts

start position in the genome

strands

strands

genome

an BSgenome object

shift_range

the shift range of PWM hits

search_point_START

Not use

Details

the hits is searched by matchPWM and the cutoff is 70%

Value

the offset of positions of CP sites after filter

Author(s)

Jianhong Ou

See Also

proximalAdjByCleanUpdTSeq, proximalAdj, PAscore


[Package InPAS version 1.16.1 Index]