get_PAscore {InPAS} | R Documentation

## calculate the CP score

### Description

calculate the CP score by using PWM of polyadenylation signal

### Usage

    get_PAscore(seqname, pos, str, idx, PWM, genome, ups = 50, dws = 50)

### Arguments

`seqname` | a character(n) vector, the chromosome/scaffold' name
`pos` | genomic positions
`str` | DNA strand
`idx` | offset position
`PWM` | An R object for a position weight matrix (PWM) for a hexamer polyadenylation signal (PAS), such as AAUAAA.
`genome` | an object of BSgenome::BSgenome
`ups` | the number of upstream bases for PAS search.
`dws` | the number of downstream bases for PAS search.

### Value

A list containing offset positions after PA score-based filtering

### Author(s)

Jianhong Ou

### See Also

`get_PAscore2()`

[Package InPAS version 2.2.0 Index]