search_proximalCPs {InPAS} | R Documentation

## search proximal CPsites

### Description

search proximal CPsites

### Usage

    search_proximalCPs(
      CPs,
      curr_UTR,
      window_size,
      MINSIZE,
      cutEnd,
      search_point_START,
      search_point_END,
      two_way = FALSE
    )

### Arguments

`CPs` | output from `search_distalCPs()` or `adjust_distalCPs()`
`curr_UTR` | GRanges for current 3' UTR
`window_size` | window size
`MINSIZE` | MINSIZE for short form
`cutEnd` | a numeric(1) between 0 and 1. The percentage of nucleotides should be removed from the end before search, 0.1 means 10 percent.
`search_point_START` | start point for searching
`search_point_END` | end point for searching
`two_way` | Search the proximal site from both direction or not.

### Value

a list

### Author(s)

Jianhong Ou

### See Also

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

[Package InPAS version 2.2.0 Index]