R/bed_to_RData.R

In LosevAMU/remapR: Bioinformatic tools to transform ReMap-data in R

#' @title Bed to RData
#' @author Alexey Solovyev
#' @description This function converts files from *.bed to .RData files.
#'
#' @param dirFrom The path to files. By default "~/tmp/RData/Input".
#'
#' @return In case of success it returns the word "Done".
#'
#' @usage bedToRData(dirFrom="")
#'
#' @examples
#' bedToRData(dirFrom="")
#'
#' @export
bedToRData <- function(dirFrom="") {

  dirTo <- path.expand("~/tmp/RData/Input")
  if (dirFrom == "") {
    dirFrom <- path.expand("~/tmp/RData/Input")
  }

  for (i in setdiff(list.files(dirFrom), grep("RData$", list.files(dirFrom), value = TRUE))) {
    print(i)
    fileNameInput <- i
    fileNameOutput <- paste(i, ".RData", sep = "")
    dirInput <- dirFrom
    # dirOutput <- dirTo
    myFileInput <- file.path(dirInput, fileNameInput)
    myFileOutput <- file.path(dirInput, fileNameOutput)

    myFrame <- read.table(file = myFileInput,
                           header = FALSE, sep = "",
                           col.names = c("Chromosome",
                                         "Begin",
                                         "End",
                                         "Conditions",
                                         "Score",
                                         "Brin",
                                         "Peak1",
                                         "Peak2",
                                         "Color_RGB"),
                           colClasses = c(NA, NA, NA, "character", NA, NA, NA, NA, "character"))

    myFrame$Score <- NULL
    myFrame$Brin <- NULL
    myFrame$Peak2 <- NULL
    myFrame$Color_RGB <- NULL

    myFrame$ID <- matrix(unlist(strsplit(myFrame$Conditions, "[.]")), ncol=3, byrow=TRUE)[,1]
    myFrame$TF <- matrix(unlist(strsplit(myFrame$Conditions, "[.]")), ncol=3, byrow=TRUE)[,2]
    myFrame$Cell_Mod <- matrix(unlist(strsplit(myFrame$Conditions, "[.]")), ncol=3, byrow=TRUE)[,3]

    myFrame$Conditions <- NULL

    save(myFrame, file=myFileOutput)

  }

  camelCaps <- "Done"
  return(camelCaps)
}