extractBoundaries: Function to extract using boundaries from domain data

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

Description

Function to extract using boundaries from domain data

Usage

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

Arguments

domains.mat	either a matrix or data.frame with at least 3 columns. First column is either of class "numeric" or "integer". The second and third columns are the start and end coordinates of domains, respectively. Required.
preprocess	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, specifying which chromosome(s) to extract domain boundaries on (ex: "CHR22"). Required.
resolution	numeric, the Hi-C data resolution that domains were called at. Ignored if preprocess is FALSE.

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,
                               preprocess=FALSE,
                               CHR=paste0("CHR",c(1:8,10:22)),
                               resolution=5000)

preciseTAD documentation built on Nov. 8, 2020, 6:51 p.m.