HiCPro2DNAlandscapeR: Export DNAlandscapeR files straight from HiC Pro Output
In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

Description Usage Arguments Value Examples

HiCPro2DNAlandscapeR takes the input files from HiC Pro output and creates a .rds and a .resolutions.txt set of files that can be visualized 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.

HiCPro2DNAlandscapeR(matrix.files, bed.files, resolutions, sampleName,
  genomeBuild = NA, splitByChr = FALSE, out.dir = "",
  drop.chrom = c("chrY", "chrM"), manual.chr = NA, manual.dist = NA,
  tempFile = TRUE, BPPARAM = BiocParallel::bpparam())

## S4 method for signature 'ANY'
HiCPro2DNAlandscapeR(matrix.files, bed.files, resolutions,
  sampleName, genomeBuild = NA, splitByChr = FALSE, out.dir = "",
  drop.chrom = c("chrY", "chrM"), manual.chr = NA, manual.dist = NA,
  tempFile = TRUE, BPPARAM = BiocParallel::bpparam())

`matrix.files`	Path to .matrix files from Hi-C Pro Output
`bed.files`	Path to .bed files from Hi-C Pro Output
`resolutions`	Character vector of the resolutions of the Hi-C output
`sampleName`	Single string of Hi-C data sample that is imported. "-HiC" will automatically be appended.
`genomeBuild`	= NA Can specify one of c("hg38", "hg19", "hg18", "mm10", "mm9", "mm8") that are built-in options for Hi-C chromosomes and distances. If not of these options are suitable, then use the `manual.chr` and `manual.dist` parameters
`splitByChr`	= FALSE Split .rds files by chromosome for faster i/o in browser?
`out.dir`	= "" The output directory to save the new tarball
`drop.chrom`	= c("chrY", "chrM") Chromosomes dropped from compression
`manual.chr`	= NA Specify a vector of chromosome names in the data
`manual.dist`	= NA Specify a same length vector as manual.chr with the chromosomal distances corresponding to each element in the manual.chr
`tempFile`	= TRUE Create a temporary file in Awk to make i/o faster and more memory efficient.
`BPPARAM`	= bpparam() Parameters to pass to bplapply

Will produce two files in the specified out.dir

#' # 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"
sampleName = "hESC1"
#HiCPro2DNAlandscapeR(matrix.files, bed.files, resolutions, sampleName = "hESC1", genomeBuild)
#HiCPro2DNAlandscapeR(matrix.files, bed.files, resolutions,
#sampleName = "hESC1", genomeBuild, splitByChr = TRUE)