proximalAdjByPWM: adjust the proximal CP sites by PWM

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 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

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