extract_hic_eigenvectors: extract_hic_eigenvectors

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

extract_hic_eigenvectors

Description

This function uses Juicer command line tools to extract first eigenvectors across chromosomes from counts data in a .hic file and outputs them to text file of the structure chr start end score where the score column contains the eigenvector elements.

Usage

extract_hic_eigenvectors(
  hicfile,
  mode = "KR",
  binsize = 250e3,
  chrs = NULL,
  gen = "Hsapiens",
  gen_ver = "hg19"
)

Arguments

hicfile	path to the input .hic file.
mode	Normalization mode to extract first eigenvectors from Allowable options are: 'NONE' for raw (normalized counts if .hic file is written using hicdc2hic or hic2icenorm_gi_list), 'KR' for Knight-Ruiz normalization, 'VC' for Vanilla-Coverage normalization and 'VC_SQRT' for square root vanilla coverage. Defaults to 'KR'.
binsize	the uniform binning size for compartment scores in bp. Defaults to 100e3.
chrs	a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes except "Y", and "M" for the specified gen and gen_ver.
gen	name of the species: e.g., default 'Hsapiens'.
gen_ver	genomic assembly version: e.g., default 'hg19'.

Value

path to the eigenvector text files for each chromosome containing chromosome, start, end and compartment score values that may need to be flipped signs for each chromosome. File paths follow gsub('.hic','_<chromosome>_eigenvectors.txt',hicfile)

Examples

eigenvector_filepaths<-extract_hic_eigenvectors(
hicfile=system.file("extdata", "eigenvector_example.hic",
package = "HiCDCPlus"),
chrs=c("chr22"),binsize=250e3,mode="NONE")

mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.