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

prepareCisPairs {sevenC}

R Documentation

Prepares motif pairs as `GInteractions` and add genomic features.

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")