extractBoundaries {preciseTAD} | R Documentation |
Function to extract using boundaries from domain data
extractBoundaries(domains.mat, preprocess = FALSE, CHR, resolution)
domains.mat |
either a |
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. |
A GRanges
object
#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)