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

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

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)