R/jDMRRegTobedGraph.R

In jlab-code/jDMR: A heuristic DMR caller for large-scale WGBS data

MethimputeRegTobedGraph.rcmethlvl <- function(regfile, out.dir) {
  cat(paste0("Reading Methimpute file: ", regfile, "\n"))
  fname <- fread(regfile, skip = 1, select = c("V1","V2","V3","V7"))
  name <- gsub(pattern = "\\.txt$", "", basename(regfile))
  fname$V2 <- format(fname$V2, scientific = FALSE) 
  fname$V3 <- format(fname$V3, scientific = FALSE)
  print(paste0("Writing to bedGraph format....",name))
  fwrite(x= fname, file=paste0(out.dir, "/", name,"-rcmethlvl.bedGraph"), sep="\t", 
         quote=FALSE, row.names=FALSE, col.names=FALSE)
}

MethimputeRegTobedGraph.stateCalls <- function(regfile, out.dir) {
  cat(paste0("Reading Methimpute file: ", regfile, "\n"))
  fname <- fread(regfile, skip = 1, select = c("V1","V2","V3","V6"))
  fname$V6<- ifelse(fname$V6 == "U", yes=0, no=1)
  name <- gsub(pattern = "\\.txt$", "", basename(regfile))
  fname$V2 <- format(fname$V2, scientific = FALSE) 
  fname$V3 <- format(fname$V3, scientific = FALSE)
  print(paste0("Writing to bedGraph format....",name))
  fwrite(x= fname, file=paste0(out.dir, "/", name,"-stateCalls.bedGraph"), sep="\t", 
         quote=FALSE, row.names=FALSE, col.names=FALSE)
}