parseLoopsRao {sevenC} | R Documentation

## Parse chromatin loops from Rao et al. 2014 as strict `GInteractions`.

### Description

Parse chromatin loops from Rao et al. 2014 as strict `GInteractions`.

### Usage

    parseLoopsRao(inFile, ...)

### Arguments

`inFile` | input file with loops
`...` | additional arguments, that will be passed to `GRanges` functions.

### Value

`GInteractions` with loops from input file.

### Examples

    # use example loop file
    exampleLoopFile <- system.file("extdata",
      "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC")

    # read loops form example file:
    gi <- parseLoopsRao(exampleLoopFile)

    # read loops with custom seqinfo object:
    customSeqInfo <- Seqinfo(seqnames = c("chr1", "chr22"),
       seqlengths = c(10^8, 10^8), isCircular = c(FALSE, FALSE),
       genome = "custom")
    gi <- parseLoopsRao(exampleLoopFile, seqinfo = customSeqInfo)

[Package sevenC version 1.7.0 Index]