R/setup_BWASPR.R

In BrendelGroup/BWASPR: Various R functions and scripts for the analyis of BWASP workflow output

#' setup_BWASPR()
#' Setting up a BWASPR analysis structure
#'
#' @param datafile A BWASP data description file consisting of rows of
#'   tab-deliminted entries with consecutive labesl for Species, Study,
#'   Sample, Replicate, Type, and BWASP mcalls file location.
#' @param parfile  A BWASPR parameter file with parameter settings used in
#'   in the analysis.
#'
#' @return A list consisting of a data frame with the data input file paths
#'         (identified as list item "datafiles") and a data frame with
#'         parameter assignments (identified as list item "parameters")
#'
#'
#' @examples
#'   mydatf <- system.file("extdata","Am.dat",package="BWASPR")
#'   myparf <- system.file("extdata","Am.par",package="BWASPR")
#'   myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
#'   myfiles$parameters[myfiles$parameters$Variable == "ASSEMBLYVERSION",2]
#'   as.numeric(myfiles$parameters[myfiles$parameters$Variable == "GENOMESIZE",2])
#'
#' @export

setup_BWASPR <- function(datafile,parfile) {
    message("... setting up BWASPR based on your data and parameter files ...")

    dfiles <- read.csv(datafile, sep="\t", skip=0, header=FALSE,
                       comment.char="#",
                       stringsAsFactors=FALSE
                      )
    colnames(dfiles) <- c("Species", "Study", "Sample", "Replicate", "Type",
                          "Source")
    pfile <- read.csv(parfile, sep="\t", skip=0, header=FALSE,
                      comment.char="#",
                      stringsAsFactors=FALSE
                     )
    colnames(pfile) <- c("Variable", "Value")
    files <- list("datafiles"=dfiles,"parameters"=pfile)
    message("... done ...")
    return(files)
}