getReadCountPerRestrictionFragment: count reads per resitrcition fragment

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

1
2
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

1
  #See the vignette	

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