olRanges: Identify Range Overlaps for IRanges and GRanges Object

In systemPipeR: systemPipeR: NGS workflow and report generation environment

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(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") 

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.