parseLoopsRao: Parse chromatin loops from Rao et al. 2014 as strict...

In ibn-salem/chromloop: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

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)

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