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")

[Package sevenC version 1.6.0 Index]