import.HiCPro.full: Compress all Hi-C Pro output data, including interchromosomal...
In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

Description Usage Arguments Value Examples

import.HiCPro.full takes output data from HiC-Pro and compresses it. All interactions will be preserved including interchromosomal. No values can be zeroed out like in the import.HiCPro function. Not recommended function to utilize for memory disk concerns but we do support importing the full data into this framework. Additionally, a temporary file cannot be generated to facilite memory constraints, so this command may fail for high resolution data.

import.HiCPro.full(matrix.files, bed.files, resolutions, sampleName,
  genomeBuild = NA, drop.chrom = c("chrY", "chrM"), manual.chr = NA,
  manual.dist = NA, BPPARAM = BiocParallel::bpparam())

## S4 method for signature 'ANY'
import.HiCPro.full(matrix.files, bed.files, resolutions,
  sampleName, genomeBuild = NA, drop.chrom = c("chrY", "chrM"),
  manual.chr = NA, manual.dist = NA, BPPARAM = BiocParallel::bpparam())

`matrix.files`	Paths to .matrix files from Hi-C Pro Output
`bed.files`	Paths 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
`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
`drop.chrom`	= c("chrY", "chrM")
`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
`BPPARAM`	= bpparam() Parameters to pass to bplapply

sparseHiCdatum of all chromosomal interactions pairwise

# 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"
# x <- import.HiCPro.full(matrix.file, bed.file, res, sampleName = "hESC1", genomeBuild)