adjust_distalCPs {InPAS} | R Documentation

## adjust distal CP sites by cleanUpdTSeq

### Description

adjust distal CP sites by cleanUpdTSeq

### Usage

    adjust_distalCPs(
      distalCPs,
      classifier,
      classifier_cutoff,
      shift_range,
      genome,
      step = 1
    )

### Arguments

`distalCPs` | the output of `search_distalCPs()`
`classifier` | An R object for Naive Bayes classifier model, like the one in the cleanUpdTSeq package.
`classifier_cutoff` | A numeric(1) vector. A cutoff of probability that a site is classified as true CP sites. The value should be between 0.5 and 1. Default, 0.8.
`shift_range` | An integer(1) vector, specifying a shift range for adjusting the proximal and distal CP sites. Default, 100. It determines the range flanking the candidate CP sites to search the most likely real CP sites.
`genome` | a BSgenome::BSgenome object
`step` | An integer (1) vector, specifying the step size used for adjusting the proximal or distal CP sites using the Naive Bayes classifier from the cleanUpdTSeq package. Default 1. It can be in the range of 1 to 10.

### Author(s)

Jianhong Ou

### See Also

`search_proximalCPs()`, `get_PAscore2()`

[Package InPAS version 2.2.0 Index]