adjust_proximalCPsByNBC {InPAS} | R Documentation

## adjust the proximal CP sites by using Naive Bayes classifier from cleanUpdTSeq

### Description

adjust the proximal CP sites by using Naive Bayes classifier from cleanUpdTSeq

### Usage

    adjust_proximalCPsByNBC(
      idx.list,
      cov_diff.list,
      seqnames,
      starts,
      strands,
      genome,
      classifier,
      classifier_cutoff,
      shift_range,
      search_point_START,
      step = 1
    )

### Arguments

`idx.list` | the offset of positions of CP sites
`cov_diff.list` | the MSE values
`seqnames` | a character(n) vector, the chromosome/scaffolds' names
`starts` | starts
`strands` | strands
`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` | adjusting step, default 1, means adjust by each base by cleanUpdTSeq.

### Details

the step for calculating is 10, can not do every base base it is really very slow.

### Value

the offset of positions of CP sites after filter

### Author(s)

Jianhong Ou

### See Also

`adjust_proximalCPsByPWM()`, `get_PAscore2()`

[Package InPAS version 2.2.0 Index]