R/functions.R

In ethevenot/r-w4m2bioc: Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

#' readw4m
#'
#' Creating a ExpressionSet object from the 3 'dataMatrix.tsv',
#' 'sampleMetadata.tsv' and 'variableMetadata.tsv' tabulated files
#'
#' @param dirC Character: directory containing the 3 .tsv files
#' @param namePatternC Character: optional file name pattern common to all three
#' file names (e.g., when you want to distinguish between two sets of files
#' within the same directory)
#' @param fileTableNamesVc Vector of characters: if your file names do not
#' contain the standard 'dataMatrix', 'sampleMetadata', and 'variableMetadata'
#' patterns (e.g. if you use 'profile', 'observation', and 'feature' instead),
#' please indicate them here
#' @param verboseL Logical: should comments be printed?
#' @return ExpressionSet instance
#' @author Etienne Thevenot, \email{etienne.thevenot@@cea.fr}
#' @examples sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
#' @rdname readw4m
#' @export
readw4m <- function(dirC,
                    namePatternC = "",
                    fileTableNamesVc = c("dataMatrix",
                                         "sampleMetadata",
                                         "variableMetadata"),
                    verboseL = TRUE) {

    tabVc <- c("dataMatrix",
               "sampleMetadata",
               "variableMetadata")

    if(!file.exists(dirC))
        stop("Directory '", dirC, "' was not found.",
             call.=FALSE)

    filVc <- character(length(tabVc))
    names(filVc) <- tabVc

    filAllVc <- list.files(dirC,
                           pattern = "^.*\\.tsv$")

    ## restricting to files with pattern
    if(namePatternC != "")
        filAllVc <- grep(namePatternC, filAllVc, value = TRUE)

    ## restricting to one file for each table
    for(tabC in tabVc) {
        namC <- fileTableNamesVc[tabVc == tabC]
        filC <- grep(namC, filAllVc, value = TRUE)
        if(length(filC) == 0) {
            stop("No file found for the ", tabC, " with ",
                 ifelse(namePatternC != "",
                        paste0("'", namC, "' pattern and "), ""),
                 "a name including '", namC, "' in the '", dirC,
                 "' directory.", call. = FALSE)
        } else if(length(filC) > 1) {
            stop("Several files found for the ", tabC, " with ",
                 ifelse(namePatternC != "", paste0("'", namC, "' pattern and "),
                        ""), "a name including '", namC, "' in the '",
                 dirC, "' directory.", call. = FALSE)
        } else {
            filVc[tabC] <- filC
            ## R standards for row and column names in matrices and data frames
            .checkRformatF(dirC, filC, verboseL)
        }
    }

    ## Loading data

    for(tabC in tabVc) {

        tabDF <- read.table(file.path(dirC, filVc[tabC]),
                            check.names = FALSE,
                            header = TRUE,
                            row.names = 1,
                            sep = "\t",
                            stringsAsFactors = FALSE)
        switch(tabC,
               dataMatrix = {
                   datMN <- as.matrix(tabDF)
               },
               sampleMetadata = {
                   samDF <- tabDF
               },
               variableMetadata = {
                   varDF <- tabDF
               })

    }

    chkL <- .checkW4mFormatF(t(datMN), samDF, varDF)

    if(chkL) {
        TRUE
    } else
        "Problem with the sample or variable names in the tables (see above)"

    eset <- ExpressionSet(assayData = datMN,
                          phenoData = new("AnnotatedDataFrame",
                              data = samDF),
                          featureData = new("AnnotatedDataFrame",
                              data = varDF),
                          experimentData = new("MIAME",
                              title = namePatternC))

    validObject(eset)

    return(eset)

}