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

Description Usage Arguments Details Value Examples

import.HiCPro takes output data from HiC-Pro and compresses it. Only intrachromosomal interactions will be preserved.

import.HiCPro(matrix.files, bed.files, resolutions, sampleName,
  genomeBuild = NA, n = 40, drop.chrom = c("chrY", "chrM"),
  manual.chr = NA, manual.dist = NA, tempFile = TRUE,
  BPPARAM = BiocParallel::bpparam())

## S4 method for signature 'ANY'
import.HiCPro(matrix.files, bed.files, resolutions, sampleName,
  genomeBuild = NA, n = 40, 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
`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
`n`	= 40 Number of off-diagonal rows to retain features to retain. If n = 0, retain the full data.
`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

Supply three vectors of equivalent length; one specifies the location of the .matrix files, one the location of the .bed files, and one the resolution of the samples for each element in that order.

This only works for one sample. Apply the function over multiple samples and then combine with the combine function to make a single object with multiple samples.

sparseHiCdatum of all intrachromosomal interactions of n diagonals

# 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(matrix.files, bed.files, resolutions, sampleName = "hESC1", genomeBuild)