getReadCountPerRestrictionFragment: count reads per resitrcition fragment

In supatt/r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Description

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

Usage

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

Arguments

object	r3Cseq 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, getBatchReadCountPerRestrictionFragment

Examples

  #See the vignette	

supatt/r3Cseq documentation built on May 3, 2019, 1:46 p.m.