getBatchReadCountPerRestrictionFragment: count reads for replicates analysis

In 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 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	

r3Cseq documentation built on Nov. 8, 2020, 6:26 p.m.