olRanges {systemPipeR} | R Documentation

## Identify Range Overlaps for IRanges and GRanges Object

### Description

Function for identifying consensus peak among two peaks sets sharing a minimum relative overlap.

### Usage

    olRanges(query, subject, output = "gr")

### Arguments

`query` | Object of class `GRanges`, which is a vector of genomic locations and associated annotations.
`subject` | Object of class `GRanges`.
`output` | By default `"gr"` returns any overlap with OL length information in an object of class `GRanges`. Also, can returns an object of class `data.frame` with `"df"`.

### Author(s)

Thomas Girke

### Examples

    ## Sample Data Sets
    grq <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges = IRanges::IRanges(seq(1, 100, by=10), end = seq(30, 120, by=10)), strand = Rle(strand(c("-", "+", "-")), c(1, 7, 2)))
    grs <- shift(grq[c(2,5,6)], 5)
    ## Run olRanges function
    olRanges(query=grq, subject=grs, output="df")
    olRanges(query=grq, subject=grs, output="gr")

[Package systemPipeR version 2.0.8 Index]