R/readPCL.R

In sagun98/mpuri: Microbiome Plotting Utilities in R (version I)

#' Read numeric data plus metadata from a .pcl file
#'
#' \code{readPCL} reads numeric data plus metadata from a .pcl file. It assumes
#' that the first row is a header. It can attempt to automatically determine
#' which rows are metadata and which are phenotype data, or the number of
#' phenotype rows can be specified explicitly.
#'
#' @param filename Fully specified path to a .pcl file
#' @param number.pheno.rows Number of rows of metadata. If
#' \code{number.pheno.rows} is NA, this function will figure out the number of
#' rows of phenotypes, under the assumption that 5 consecutive rows of numeric
#' values signifies the start of the numeric data at the startn of those
#' consecutive rows. If \code{number.pheno.rows} is specified, it tells the
#' program how many rows at the start of the file (not including the header) are
#' phenotype data.  
#' @param ... Additional arguments passed on to \code{\link{read.table}}.
#' @return Returns a list object containing two elements: 
#' \enumerate{
#'     \item phenodat, a dataframe containing the potentially non-numeric 
#'       phenotype data.
#'     \item  numericdat, a matrix containing the numeric expression data.
#' }

readPCL <- function(filename, number.pheno.rows = NA, ...) {

    whichPheno <- function(filename, n, consecutive.numeric = 0, ...) {
        if (consecutive.numeric >= 5) {
            return(n - consecutive.numeric + 1)
        }
        else {
            one.row <- read.table(filename, skip = n, nrows = 1, ...)
            one.row <- t(one.row)[, 1]
            if (is.numeric(one.row)) {
                return(whichPheno(filename, n + 1, consecutive.numeric + 1,
                                  ...)) 
            }
            else {
                return(whichPheno(filename, n + 1, consecutive.numeric, ...))
            }
        }
    }

    if (is.na(number.pheno.rows)) {
        number.pheno.rows <- whichPheno(filename, n = 1, 
                                        consecutive.numeric = 0, ...)
    }
    phenodat <- read.delim(filename, nrows = number.pheno.rows, header = TRUE,
                           ...)
    numericdat <- read.delim(filename, skip = number.pheno.rows + 1, header =
                             FALSE, row.names=1, ...)
    colnames(numericdat) <- colnames(phenodat)[-1]
    numericdat <- as.matrix(numericdat)
    tmp.file <- tempfile()
    write.table(t(phenodat), file = tmp.file, col.names=FALSE, sep=",")
    phenodat <- read.csv(tmp.file, row.names = 1, ...)
    file.remove(tmp.file)
    output <- list(phenodat = phenodat, numericdat = numericdat)
    return(output)
}