## ----load_packages, include=FALSE---------------------------------------- knitr::opts_knit$set(progress = TRUE, verbose = TRUE) library(hicrep) data("HiCR1") data("HiCR2") ## ------------------------------------------------------------------------ dim(HiCR1) HiCR1[1:10,1:10] ## ---- eval=TRUE---------------------------------------------------------- Pre_HiC <- prep(HiCR1, HiCR2, 1000000, 1, 5000000) head(Pre_HiC) ## ---- eval=TRUE---------------------------------------------------------- h_hat <- htrain(HiCR1, HiCR2, 1000000, 5000000, 0:2) h_hat ## ------------------------------------------------------------------------ #check total number of reads before adjustment sum(HiCR1[,-c(1:3)]) DS_HiCR1 <- depth.adj(HiCR1, 200000, 1000000, out = 0) #check total number of reads after adjustment sum(DS_HiCR1[,-c(1:3)]) ## ---- eval=TRUE---------------------------------------------------------- SCC.out = get.scc(Pre_HiC, 1000000, 5000000) #SCC score SCC.out[[3]] #Standard deviation of SCC SCC.out[[4]] sessionInfo()