#' read.gdm
#'
#' @param path character, location of the *.gloDatamix files
#' @param header logical, gloDataMix files with or without header?
#' @param input character, 'gloDatamix' or 'csv'
#'
#' @return concatenates all gloDatamix files from a location in one data.frame
#' @author Daniel Münch <daniel@@muench.bio>
#'
#' @export
#' @examples \dontrun{
#' data <- read.gdm("./80109-final_all/", header=F)
#' }
read.gdm <- function(path,
header = TRUE,
input = "gloDatamix" # gloDatamix for gloDatamix-files, "csv" for knime output
) {
wd <- getwd()
setwd(path)
if (input == "gloDatamix") nfile <- dir(pattern = "(gloDatamix)$", ignore.case = T)
if (input == "csv") nfile <- dir(pattern = "(csv)$", ignore.case = T)
if (length(nfile) < 1 & input == "gloDatamix") warning(paste("No *.gloDatamix files found @", getwd(),", please check folder and filenames (must end with gloDatamix)\n\n"))
if (length(nfile) < 1 & input == "csv") warning(paste("No *.csv files found @", getwd(),", please check folder and filenames (must end with csv)\n\n"))
combdata <- numeric()
for (i in 1:length(nfile)) {
if (input == "gloDatamix") tmp <- read.table(nfile[i], sep="\t", header=header)
if (input == "csv") tmp <- read.csv(nfile[i], header=header)
combdata <- rbind(combdata, tmp)
message(nfile[i])
}
setwd(wd)
return(combdata)
}
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