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

Description Usage Arguments Value Examples

View source: R/parseInteractions.R

Description

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

Usage

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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

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# 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)

sevenC documentation built on Nov. 8, 2020, 5:35 p.m.