subsetRegion {diffloop} | R Documentation

## Extract region from loops object

### Description

`subsetRegion` takes a `loops` object and a `GRanges` object and returns a `loops` object where both anchors map inside the `GRanges` coordinates by default. Once can specify where only one anchor is in the region instead.

### Usage

    subsetRegion(dlo, region, nanchors)

    ## S4 method for signature 'loops,GRanges,numeric'
    subsetRegion(dlo, region, nanchors)

    ## S4 method for signature 'loops,GRanges,missing'
    subsetRegion(dlo, region, nanchors)

### Arguments

`dlo` | A loops object to be subsetted
`region` | A GRanges object containing region of interest
`nanchors` | Number of anchors to be contained in GRanges object. Default 2

### Details

By default, `nachors = 2`, meaning both anchors need to be in the region for the loop to be preserved when extracting. However, by specifying a numeric 1, interactions with either the left or right anchor will be extracted. Loops with both anchors in the region will be excluded (exclusive `or`). To get an inclusive `or`, take the union of subsetting both with 1 and 2.

### Value

A loops object

### Examples

    # Grab region chr1:36000000-36100000
    library(GenomicRanges)
    regA <- GRanges(c('1'),IRanges(c(36000000),c(36100000)))
    rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
    load(rda)
    # Both anchors in region
    loops.small.two <- subsetRegion(loops.small, regA)
    #Only one anchor in region
    loops.small.one <- subsetRegion(loops.small, regA, 1)
    #Either one or two anchors in region
    loops.small.both <- union(loops.small.one, loops.small.two)

[Package diffloop version 1.8.0 Index]