prepareCisPairs: Prepares motif pairs as 'GInteractions' and add genomic...

In ibn-salem/chromloop: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Description

Prepares motif pairs as GInteractions and add genomic features.

Usage

prepareCisPairs(motifs, maxDist = 1e+06, scoreColname = "score")

Arguments

motifs	GRanges object with motif locations.
maxDist	maximal distance in base-pairs between pairs of ranges as single numeric value.
scoreColname	Character as name the metadata column in with motif score.

Value

An GInteractions object with motif pairs and annotations of distance, strand orientation, and motif scores.

Examples

# build example GRanges as anchors
anchorGR <- GRanges(
 rep("chr1", 4),
 IRanges(
   c(1, 5, 20, 14),
   c(4, 8, 23, 17)
 ),
 strand = c("+", "+", "+", "-"),
 score = c(5, 4, 6, 7)
)



# prepare candidates
gi <- prepareCisPairs(anchorGR)


# prepare candidates using a mimial distance of 10 bp
gi <- prepareCisPairs(anchorGR, maxDist = 10)

# prepare candidates using an alternative score value in anchors
anchorGR$myScore <- rnorm(length(anchorGR))
gi <- prepareCisPairs(anchorGR, scoreColname = "myScore")

ibn-salem/chromloop documentation built on May 18, 2019, 1:29 a.m.