#' Reading MaxQuant Output
#'
#' Reads in "summary.txt" output.
#'
#'@param path character path to the folder containing "summary.txt file".
#' It should be in "{raw files folder}/combined/txt"
#'
#' @return data.frame
#' @export readMaxQuantSummary
#' @examples
#'
#' fpath <- list.files(path = path,
#' pattern = "summary.txt",
#' full.names = TRUE)
#' stopifnot(length(fpath) == 1)
#' smmr <- readMaxQuantSummary(fpath)
#'
readMaxQuantSummary <- function (path) {
fpath <- list.files(path = path, pattern = "summary.txt",
full.names = TRUE)
stopifnot(length(fpath) == 1)
smmr <- read.delim(fpath, check.names = FALSE, stringsAsFactors = FALSE)
smmr <- smmr[seq_len(nrow(smmr) - 1), ] # drop last row
if (any(smmr$Experiment == "")) {
warning("Dropping rows from \"summary.txt\" with missing experiment label. Please double check.")
smmr <- smmr[which(smmr$Experiment != ""), ]
}
warning(paste("Found", nrow(smmr), "datasets"))
smmr <- data.frame(dataset.name = smmr[, "Raw file"],
row.names = smmr[, "Experiment"],
stringsAsFactors = FALSE)
return(smmr)
}
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