regionOverlap {Ringo} | R Documentation

## Function to compute overlap of genomic regions

### Description

Given two data frames of genomic regions, this function computes the base-pair overlap, if any, between every pair of regions from the two lists.

### Usage

    regionOverlap(xdf, ydf, chrColumn = "chr", startColumn = "start",
                  endColumn = "end", mem.limit=1e8)

### Arguments

`xdf` | `data.frame` that holds the first set of genomic regions
`ydf` | `data.frame` that holds the first set of genomic regions
`chrColumn` | character; what is the name of the column that holds the chromosome name of the regions in `xdf` and `ydf`
`startColumn` | character; what is the name of the column that holds the start position of the regions in `xdf` and `ydf`
`endColumn` | character; what is the name of the column that holds the start position of the regions in `xdf` and `ydf`
`mem.limit` | integer value; what is the maximal allowed size of matrices during the computation

### Value

Originally, a matrix with `nrow(xdf)` rows and `nrow(ydf)` columns, in which entry `X[i,j]` specifies the length of the overlap between region `i` of the first list (`xdf`) and region `j` of the second list (`ydf`). Since this matrix is very sparse, we use the `dgCMatrix` representation from the `Matrix` package for it.

### Note

The function only return the absolute length of overlapping regions in base-pairs. It does not return the position of the overlap or the fraction of region 1 and/or region 2 that overlaps the other regions.

The argument `mem.limit` is not really a limit to used RAM, but rather the maximal size of matrices that should be allowed during the computation. If larger matrices would arise, the second regions list is split into parts and the overlap with the first list is computed for each part. During computation, matrices of size `nrow(xdf)` times `nrow(ydf)` are created.

### Author(s)

Joern Toedling

### See Also

`dgCMatrix-class`

### Examples

      ## toy example:
      regionsH3ac <- data.frame(chr=c("chr1","chr7","chr8","chr1","chrX","chr8"), start=c(100,100,100,510,100,60), end=c(200, 200, 200,520,200,80))
      regionsH4ac <- data.frame(chr=c("chr1","chr2","chr7","chr8","chr9"),
    start=c(500,100,50,80,100), end=c(700, 200, 250, 120,200))

      ## compare the regions first by eye
      ##  which ones do overlap and by what amount?
      regionsH3ac
      regionsH4ac

      ## compare it to the result:
      as.matrix(regionOverlap(regionsH3ac, regionsH4ac))
      nonzero(regionOverlap(regionsH3ac, regionsH4ac))

[Package Ringo version 1.44.0 Index]