Output: Take the bin number of the detected TAD boundaries as input,...
In bioinfo-lab/TADBD: A sensitive and fast tool for detection of TAD boundaries

Description Usage Arguments Examples

View source: R/Output.R

Take the bin number of the detected TAD boundaries as input, and output the TAD boundaries in an optional form between text file and graphical heatmap.

1	Output(df_result, species = "hg19", chr = "chr1", resolution = 50000, outxtfile=NULL, bheatmap = FALSE, heatmapfile=NULL, hicmat=NULL, map_start = 0, map_end = 10000000, l_color="blue", l_width=2.5)

`df_result`	a dataframe consisting of the bin number of the detected TAD boundaries by TADBD function.
`species`	species name, including "hg19", "hg38", "mm9" and "mm10".
`chr`	chromosome name.
`resolution`	resolution of of Hi-C matrix.
`outxtfile`	the path and name of output text file.
`bheatmap`	if a heatmap with TAD tracks is shown, bheatmap = TRUE, otherwise bheatmap = FALSE(default).
`heatmapfile`	the path and name of output heatmap file, the argument needs to be specifie only when bheatmap = TRUE.
`hicmat`	a dense contact matrix by DataLoad, the argument needs to be specified only when bheatmap = TRUE.
`map_start`	the starting coordinate of the heatmap,value is an integer multiple of resolution and the default is 0.
`map_end`	the ending coordinate of the heatmap,value is an integer multiple of resolution and the default is 10000000.
`l_color`	color of the TAD track.
`l_width`	width of the TAD track.

#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)
#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)
#Output two text files, one is for detected TAD boundaries, the other for intermediate peaks
Output(df_result, species, chr, resolution, outxtfile="./result")
#Output two text files and a heatmap with TAD boundary tracks, the parameters of heatmap include starting and ending coordinates, as well as the color and the width of tracks
Output(df_result, species, chr, resolution, outxtfile="./result", bheatmap = TRUE, heatmapfile="./heatmap", hicmat, map_start=0, map_end=10000000, l_color="blue", l_width=2.5)