searchProximalCPs {InPAS} | R Documentation

## search proximal CPsites

### Description

search proximal CPsites

### Usage

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

### Arguments

`CPs` | output of searchDistalCPs or distalAdj
`curr_UTR` | GRanges of current 3UTR
`window_size` | window size
`MINSIZE` | MINSIZE for short form
`cutEnd` | how many 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

`proximalAdj`, `polishCPs`, `proximalAdjByPWM`, `proximalAdjByCleanUpdTSeq`, `PAscore`,`PAscore2`

[Package InPAS version 1.16.3 Index]