DataLoad: Load a Hi-C matrix file in sparse or dense format, and output...

In bioinfo-lab/TADBD: A sensitive and fast tool for detection of TAD boundaries

Description

Load a Hi-C matrix file in sparse or dense format, and output the dense contact matrix.

Usage

DataLoad(hicdata, bsparse, species, chr, resolution)

Arguments

hicdata	a Hi-C matrix file.
bsparse	if the Hi-C matrix is in sparse format, bsparse = TRUE, otherwise bsparse = FALSE.
species	species name, including "hg19", "hg38", "mm9" and "mm10", the argument needs to be specified only when bsparse = TRUE.
chr	chromosome name, such as "chr1", "chr22", "chrX" and "chrY", the argument needs to be specified only when bsparse = TRUE.
resolution	resolution of Hi-C matrix, the argument needs to be specified only when bsparse = TRUE.

Value

A dense contact matrix.

Examples

#Load R package TADBD
library(TADBD)
#Configuration of the parameters, including species, chromsome and resolution
species <- "hg19"
chr <- "chr18"
resolution <- 50000
#Close scientific notation
options(scipen = 999)
#Specify Hi-C data to be loaded
data(hicdata)
#Load a Hi-C contact matrix file in a dense format
hicmat <- DataLoad(hicdata, bsparse = FALSE, species, chr, resolution)

bioinfo-lab/TADBD documentation built on March 15, 2020, 8:53 a.m.