KanduriC / GenomicOverlap

To compute the cumulative overlap of the regions between two files containing genomic intervals

GenomicOverlap

Author: Chakravarthi Kanduri

compute_overlap function

This R function computes the cumulative overlap of the regions between two files containing genomic intervals.

Usage

compute_overlap (fileA, fileB)

Arguments

• fileA, fileB: Tab-delimited files with genomic intervals sorted in ascending order.
• genomeSize: The size of the reference genome in bases; numeric; defaults to 10000000.
• startCol, endCol: The column numbers of start and end coordinates in files; numeric; defaults to 1 and 2.

Examples

source("computeOverlap.R")
compute_overlap("A.txt","B.txt")
compute_overlap(newfile1,newfile2,genomeSize=20000000,startCol=2,endCol=3)