## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=TRUE---------------------------------------------------------------- library(DMCFB) fn <- list.files(system.file("extdata",package = "DMCFB")) fn.f <- list.files(system.file("extdata",package="DMCFB"), full.names=TRUE) OBJ <- readBismark(fn.f, fn, mc.cores = 2) cdOBJ <- DataFrame(Cell = factor(c("BC", "TC","Mono"), levels = c("BC", "TC", "Mono")), row.names = c("BCU1568","BCU173","BCU551")) colData(OBJ) <- cdOBJ OBJ ## ----eval=TRUE, message=FALSE------------------------------------------------- library(DMCFB) set.seed(1980) nr <- 1000 nc <- 8 metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr) methc <- matrix(rbinom(n=nr*nc,c(metht),prob = runif(nr*nc)),nr,nc) methl <- methc/metht 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]) OBJ2 <- cBSDMC(rowRanges=r1,methReads=methc,totalReads=metht, methLevels=methl,colData=cd1) OBJ2 ## ----eval=FALSE--------------------------------------------------------------- # library(DMCFB) # start.time <- Sys.time() # path0 <- "..//BCData/" # provide the path to the files # namelist.new <- list.files(path0,pattern="blk",full.names=F) # namelist.new.f <- list.files(path0,pattern="blk",full.names=T) # type <- NULL # for(i in seq_along(namelist.new)){ # type[i] <- unlist(strsplit(namelist.new[i], split=c('_'), fixed=TRUE))[2] # } # type # table(type) # indTC <- which(type=="TC") # indBC <- which(type=="BC") # indMono <- which(type=="Mono") # namelist.new <- namelist.new[c(indBC,indMono,indTC)] # namelist.new.f <- namelist.new.f[c(indBC,indMono,indTC)] # BLKDat <- readBismark(namelist.new.f, namelist.new, mc.cores = 2) # colData1 <- DataFrame(Group = factor( # c(rep("BC",length(indBC)), rep("Mono",length(indMono)), # rep("TC", length(indTC))), levels = c("BC", "Mono", "TC")), # row.names = colnames(BLKData)) # colData(BLKDat) <- colData1 # BLK.BC.Mono.TC <- sort(BLKDat) # DMC.obj = findDMCFB(object = BLKDat, bwa = 30, bwb = 30, nBurn = 300, nMC = 300, # nThin = 1, alpha = 5e-5, pSize = 500, sfiles = FALSE) ## ----fig.width=6-------------------------------------------------------------- library(DMCFB) set.seed(1980) nr <- 1000 nc <- 8 metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr) methc <- matrix(rbinom(n=nr*nc,c(metht),prob = runif(nr*nc)),nr,nc) methl <- methc/metht 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 <- cBSDMC(rowRanges=r1,methReads=methc,totalReads=metht, methLevels=methl,colData=cd1) OBJ2 = findDMCFB(object = OBJ1, bwa = 30, bwb = 30, nBurn = 10, nMC = 10, nThin = 1, alpha = 0.05, pSize = 500, sfiles = FALSE) plotDMCFB(OBJ2, region = c(1,400), nSplit = 2) ## ----------------------------------------------------------------------------- sessionInfo()