computeBoundaryScores: Compute boundary scores for genomic loci in between anchors

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

computeBoundaryScores determines the boundary scores corresponding to the Genomic region either in bewteen pairs of anchors. To achieve this, the number of PETs for a set of samples (default is all = 0) is summed over a window (default 1MB) on the left (A) and the right (B) of gap. Thus sum of the number of PETs in these windows is devided by the number of PETs that span the two loci, plus 1 (C). A larger value corresponds to a stronger boundary.

Usage

computeBoundaryScores(dlo, samples = 0, windowSize = 5e+05)

## S4 method for signature 'loops'
computeBoundaryScores(dlo, samples = 0,
  windowSize = 5e+05)

Arguments

dlo	A loops object
samples	= 0 Vector indexing which samples should be used. 0 is all
windowSize	= 500000 BP length on left and right of putative boundary to define A/B

Details

Warning: this function is slow; there is a progress bar outputted to give an anticipated runntime.

Value

A GRanges object with genomic loci and boundary scores in the mcols

Examples

# Return the width for loops 
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
# BS <- computeBoundaryScores(loops.small, samples = 0, windowSize = 500000)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.