get.site.count {DBChIP} | R Documentation

## Get site count

### Description

Count number of reads around each binding site

### Usage

    get.site.count(dat, subtract.input=FALSE, window.size = 250)

### Arguments

`dat` | a list with the following items: consensus.site, chip.list, input.list, matching.input.names, norm.factor.vec. Description of the items can be found in the return value of `DBChIP`.
`subtract.input` | logical. Whether input will be subtracted from ChIP when counting the binding reads. Default is FALSE.
`window.size` | the window size to count reads around each binding site. Default 250 bp.

### Details

The read count for each binding site is defined as the sum of the number of 5' ends on the positive strand within the upstream window `[s-w, s-1]` and the number of 5' ends on the negative strand within the downstream window `[s+1, s+w]`, where `s` is a consensus site position and `w` is the window size parameter.

### Value

This function return the incoming `dat` with the new component:

`site.count` | a matrix of read counts for each site (row) and each ChIP library (column).

### See Also

`DBChIP`

[Package DBChIP version 1.31.0 Index]