load_mat: Load a Hi-C matrix from a file

In 3DGenomes/TADpole: Call hierarchical TADs

Description

Load a Hi-C matrix from a file

Usage

load_mat(
  mat_file,
  chr,
  start,
  end,
  resol,
  bad_frac = 0.01,
  centromere_search = FALSE
)

Arguments

mat_file	path to the input file. Must be in a tab-delimited matrix format.
chr	string with the chromosome name.
start	numeric start position of the region or of the chromosome.
end	numeric end position of the region or of the chromosome.
resol	numeric resolution/binning of the Hi-C experiment.
bad_frac	fraction of the matrix to falg as bad rows/columns.
centromere_search	split the matrix by the centrormere into two, smaller matrices representing the chromosomal arms. Useful when working with big (>15000 bins) datasets.

Examples

mat_file <- system.file("extdata", "raw_chr18:460-606_20kb.tsv", package = "TADpole")
mat <- load_mat(mat_file, chr = "chr18", start = 496, end = 606, resol = 20000)

3DGenomes/TADpole documentation built on Jan. 30, 2020, 8:17 p.m.