exportDNAlandscapeR: Export sparseHiCdatum to DNAlandscapeR files

In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

Description

exportDNAlandscapeR takes a sparseHiCdatum object and produces two files, a .rds and a .sparseHiC.meta file that can be used in DNAlandscapeR (dnalandscaper.aryeelab.org). If splitByChr is specified as TRUE, will create a folder with the sample name and an .rds of each chromosome for faster i/o. These split files can only be linked via a bucket in DNAlandscapeR.

Usage

exportDNAlandscapeR(dat, newSampleName = "", out.dir = "",
  splitByChr = FALSE)

## S4 method for signature 'sparseHiCdatum'
exportDNAlandscapeR(dat, newSampleName = "",
  out.dir = "", splitByChr = FALSE)

Arguments

dat	A sparseHiCdatum object
newSampleName	= "" New sample name for the object, if desired. Current one in the object is used by default.
out.dir	= "" The output directory to save the new tarball
splitByChr	= FALSE Split .rds files by chromosome for faster i/o in browser?

Value

Will produce two files in the specified out.dir

Examples

# matrix.files <- paste(system.file("extdata", package = "processedHiCdata"),
#"HiC-Pro/hESC_Rep1/hESC_Rep1_1000000_iced.matrix", sep = "/")
#bed.files <- paste(system.file("extdata", package = "processedHiCdata"),
#"HiC-Pro/hESC_Rep1/hESC_Rep1_1000000_abs.bed", sep = "/")
genomeBuild <- "hg19"
resolutions <- "1000000"
#exportDNAlandscapeR(matrix.files, bed.files, resolutions,
#sampleName = "hESC1", genomeBuild, splitByChr = TRUE)

aryeelab/sparseHiC documentation built on May 12, 2019, 3:43 a.m.