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 1.12.0 Index]