extractBoundaries: Function to extract boundaries from domain data.

In stilianoudakis/preciseTAD: preciseTAD: A machine learning framework for precise TAD boundary prediction

Description

Function to extract boundaries from domain data.

Usage

extractBoundaries(domains.mat, filter = FALSE, CHR, resolution)

Arguments

domains.mat	either a matrix or data.frame with at least 3 columns. First column is chromosome number/character (1, 2, 3, X) or ID (chr1, chr2). Non-autosomal/sex chromosomes will be filtered. The second and third columns are the start and end coordinates of the domains, respectively. Note these are coordinates of the domain anchor centers, not anchors. Only the first three columns are used. Required.
filter	logical, indicating whether or not domains exceeding 2mb in width or smaller than 2*(the specified resolution) should be filtered out (default is FALSE, all boundaries will be used). Required.
CHR	character vector, specifying which chromosome(s) to extract domain boundaries on (ex: "chr22", case ignored). Unused seqnames are dropped. Required.
resolution	numeric, the Hi-C data resolution that domains were called at. Ignored if filter is FALSE, required otherwise.

Value

A GRanges object

Examples

#Read in domain data from ARROWHEAD at 5 kb for GM12878
data("arrowhead_gm12878_5kb")
#Extract unique boundaries for CHRs 1-8 and 10-22
bounds.GR <- extractBoundaries(domains.mat=arrowhead_gm12878_5kb,
                               filter=FALSE,
                               CHR=paste0("CHR",c(1:8,10:22)),
                               resolution=5000)

stilianoudakis/preciseTAD documentation built on Sept. 23, 2021, 9:36 p.m.