TADBD: Take a dense contact matrix as input, and output the bin...

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

Description

Take a dense contact matrix as input, and output the bin number of TAD boundaries on the contact matrix.

Usage

TADBD(hicmat, template.sizes = c(4,5,6), bstatfilter = TRUE)

Arguments

hicmat	a contact matrix by DataLoad function.
template.sizes	a vector consisting of multiple template sizes, with a default value of c(4, 5, 6).The vector can also be specified by user, for example: c(3, 4, 5, 6).
bstatfilter	if statistical filtering is involved, bstatfilter = TRUE (default), otherwise bstatfilter = FALSE.

Value

A dataframe consisting of the bin number of the detected TAD boundaries.

Examples

#Load R package TADBD
library(TADBD)
#Configuration of the parameters, including species, chromsome and resolution
species <- "hg19"
chr <- "chr18"
resolution <- 50000
#Specify Hi-C data to be loaded
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)
#Detect TAD boundaries on the loaded contact matrix using TADBD method using default parameter configuration, that is template.sizes = c(4,5,6), bstatfilter = TRUE
df_result <- TADBD(hicmat)

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