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 1.20.0 Index]