parseLoopsTang: Parse chromatin interactions from Tang et al. 2015 as...

Description Usage Arguments Details Value Examples

Description

Reads pairwise ChIA-PET interaction from an input file.

Usage

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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

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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)

ibn-salem/chromloop documentation built on May 18, 2019, 1:29 a.m.