proximalAdj {InPAS} | R Documentation

## adjust the proximal CP sites

### Description

adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq

### Usage

    proximalAdj(CPs, MINSIZE, PolyA_PWM, genome, classifier, classifier_cutoff,
                shift_range, search_point_START, step=1)

### Arguments

`CPs` | the outputs of searchProximalCPs
`MINSIZE` | min size for short from
`PolyA_PWM` | PolyA position weight metrix
`genome` | a BSgenome object
`classifier` | cleanUpdTSeq classifier
`classifier_cutoff` | cutoff value of the classiffier
`shift_range` | the searching range for the better CP sites
`search_point_START` | just in case there is no better CP sites
`step` | adjust step, default 1, means adjust by each base by cleanUpdTSeq.

### Value

keep same as searchProximalCPs, which can be handled by polishCPs.

### Author(s)

Jianhong Ou

### See Also

`searchProximalCPs`, `polishCPs`, `proximalAdjByPWM`, `proximalAdjByCleanUpdTSeq`, `PAscore`,`PAscore2`

[Package InPAS version 1.20.0 Index]