get_PAscore2 {InPAS} | R Documentation

## calculate the CP score

### Description

calculate CP score by cleanUpdTSeq

### Usage

    get_PAscore2(
      seqname,
      pos,
      str,
      idx,
      idx.gp,
      genome,
      classifier,
      classifier_cutoff
    )

### Arguments

`seqname` | a character(1) vector, the chromosome/scaffold's name
`pos` | genomic positions
`str` | DNA strand
`idx` | offset position
`idx.gp` | group number of the offset position
`genome` | an object of BSgenome::BSgenome
`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.

### Value

a data frame

### Author(s)

Jianhong Ou

### See Also

`get_PAscore()`

[Package InPAS version 2.2.0 Index]