adjust_proximalCPs {InPAS} | R Documentation

## adjust the proximal CP sites

### Description

adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq

### Usage

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

### Arguments

`CPs` | the outputs of `search_proximalCPs()`
`MINSIZE` | min size for short from
`PolyA_PWM` | PolyA position weight matrix
`genome` | a BSgenome::BSgenome object
`classifier` | cleanUpdTSeq classifier
`classifier_cutoff` | cutoff value of the classifier
`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 `search_proximalCPs()`, which can be handled by `polish_CPs()`.

### Author(s)

Jianhong Ou

### See Also

`search_proximalCPs()`, `polish_CPs()`, `adjust_proximalCPsByPWM()`, `adjust_proximalCPsByNBC()`, `get_PAscore()`,`get_PAscore2()`

[Package InPAS version 2.2.0 Index]