getBatchReadCountPerWindow: count reads per window size 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 window size for replicates analysis

Usage

getBatchReadCountPerWindow(object,windowSize=5e3,nFragmentExcludedReadsNearViewpoint=2,mode=c("non-overlapping", "overlapping"))

Arguments

object	r3CseqInBatch object
windowSize	Numeric. non-overlapping window size for counting reads (default=5e3)
nFragmentExcludedReadsNearViewpoint	Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)
mode	character. The window-based modes analysis (default="non-overlapping")

Value

The RangedData represents the number of reads per each window size

Author(s)

S. Thongjuea

See Also

getReadCountPerRestrictionFragment, getBatchReadCountPerRestrictionFragment, getReadCountPerWindow,

Examples

  #See the vignette	

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