## ---- eval=TRUE, message=FALSE------------------------------------------- library(DMCHMM) fn <- list.files(system.file("extdata",package = "DMCHMM")) fn.f <- list.files(system.file("extdata",package="DMCHMM"), full.names=TRUE) OBJ <- readBismark(fn.f, fn) cdOBJ <- DataFrame(Cell = factor(c("BC", "TC","Mono"), labels = c("BC", "TC", "Mono")), row.names = c("BCU1568","BCU173","BCU551")) colData(OBJ) <- cdOBJ OBJ ## ---- eval=TRUE, message=FALSE------------------------------------------- nr <- 150; nc <- 8 metht <- matrix(as.integer(runif(nr * nc, 0, 20)), nr) methc <- matrix(rbinom(n=nr*nc,c(metht),prob = runif(nr*nc)),nr,nc) r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width=1), strand="*") names(r1) <- 1:nr cd1 <- DataFrame(Group=rep(c("G1","G2"),each=nc/2),row.names=LETTERS[1:nc]) OBJ1 <- cBSData(rowRanges=r1,methReads=methc,totalReads=metht,colData=cd1) OBJ1 ## ---- eval=TRUE, message=FALSE------------------------------------------- OBJ2 <- methHMEM(OBJ1, MaxK=2) OBJ2 ## ---- eval=TRUE, message=FALSE------------------------------------------- OBJ3 <- methHMMCMC(OBJ2) OBJ3 ## ---- eval=TRUE, message=FALSE------------------------------------------- OBJ4 <- findDMCs(OBJ3) head(metadata(OBJ4)$DMCHMM)