adjust_proximalCPsByPWM: adjust the proximal CP sites by matching PWM

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

adjust the proximal CP sites by matching PWM

Description

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

Usage

adjust_proximalCPsByPWM(
  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	a character(n) vector, the chromosome/scaffolds' names
starts	start position in the genome
strands	strands
genome	an BSgenome::BSgenome object
shift_range	the shift range of PWM hits
search_point_START	Not use

Details

the hits is searched by Biostrings::matchPWM() and the cutoff is 70\

Value

the offset of positions of CP sites after filter

Author(s)

Jianhong Ou

See Also

adjust_proximalCPsByNBC(), get_PAscore()

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.