adjust_proximalCPsByPWM {InPAS} | R Documentation

## 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()`

[Package InPAS version 2.2.0 Index]