parseLoopsTang {sevenC} | R Documentation

## Parse chromatin interactions from Tang et al. 2015 as `GInteractions`.

### Description

Reads pairwise ChIA-PET interaction from an input file.

### Usage

    parseLoopsTang(inFile, ...)

### Arguments

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

### Details

It reads files with the following tab-delimited format:

chr12 | 48160351 | 48161634 | chr12 | 48230665 | 48232848 | 27
chr7 | 77284664 | 77285815 | chr7 | 77388242 | 77388928 | 7
chr4 | 128459961 | 128460166 | chr4 | 128508304 | 128509082 | 4

This file format was used for ChIA-PET interaction data by Tang et al. 2015 http://dx.doi.org/10.1016/j.cell.2015.11.024. The last column of input file is added as annotation column with colname "score".

### Value

An `GInteractions` with loops from input file.

### Examples

    exampleLoopTang2015File <- system.file("extdata",
       "ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt",
       package = "sevenC")

    gi <- parseLoopsTang(exampleLoopTang2015File)

    # 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 <- parseLoopsTang(exampleLoopTang2015File, seqinfo = customSeqInfo)

[Package sevenC version 1.8.0 Index]