#' @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)
}
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