getBatchReadCountPerRestrictionFragment {r3Cseq} | R Documentation

## count reads for replicates analysis

### Description

Counts the number of reads from 3C-Seq data per each restriction fragment for replicates analysis

### Usage

    getBatchReadCountPerRestrictionFragment(object,getReadsMethod = c("wholeReads", "adjacentFragmentEndsReads"),
    			nFragmentExcludedReadsNearViewpoint=2)

### Arguments

`object` | r3CseqInBatch object
`getReadsMethod` | character. To count all reads found in the particular restriction fragment uses wholeReads option. To count reads found around the edge of restriction fragment both 5'utr and 3'utr uses adjacentFragmentEndsReads option (default=wholeReads)
`nFragmentExcludedReadsNearViewpoint` | Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)

### Value

The RangedData represents the number of reads per each restriction fragment

### Author(s)

S. Thongjuea

### See Also

getReadCountPerWindow, getReadCountPerRestrictionFragment

### Examples

      #See the vignette

[Package r3Cseq version 1.26.0 Index]