## ----set-options, echo=FALSE, cache=FALSE------------------------------------- knitr::opts_chunk$set(warnings = FALSE, message = FALSE) ## ----------------------------------------------------------------------------- #if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") #BiocManager::install(c("ExperimentHub"), version = "3.12") library(ExperimentHub) library(preciseTAD) library(preciseTADhub) ## ----------------------------------------------------------------------------- #Initialize ExperimentHub hub <- ExperimentHub() query(hub, "preciseTADhub") myfiles <- query(hub, "preciseTADhub") CHR22_GM12878_5kb_Arrowhead <- readEH(chr = "CHR22", cl = "GM12878", gt = "Arrowhead", source = myfiles) ## ----------------------------------------------------------------------------- data("tfbsList") # Restrict the data matrix to include only SMC3, RAD21, CTCF, and ZNF143 tfbsList_filt <- tfbsList[names(tfbsList) %in% c("Gm12878-Ctcf-Broad", "Gm12878-Rad21-Haib", "Gm12878-Smc3-Sydh", "Gm12878-Znf143-Sydh")] names(tfbsList_filt) <- c("Ctcf", "Rad21", "Smc3", "Znf143") # Run preciseTAD set.seed(123) pt <- preciseTAD(genomicElements.GR = tfbsList_filt, featureType = "distance", CHR = "CHR22", chromCoords = list(17000000, 19000000), tadModel = CHR22_GM12878_5kb_Arrowhead, threshold = 1.0, verbose = FALSE, parallel = NULL, DBSCAN_params = list(10000, 3), flank = 5000) pt