R/combineData.R

In cn.farms: cn.FARMS - factor analysis for copy number estimation

#' Combine two ExpressionSet objects
#' 
#' Suitable for SNP or non-polymorphic data which were already processed with 
#' single locus FARMS
#' 
#' @param object01 An instance of \code{\link[Biobase:class.ExpressionSet]{ExpressionSet}}
#' either with SNP or non-polymorphic data
#' @param object02 An instance of \code{\link[Biobase:class.ExpressionSet]{ExpressionSet}}
#' either with SNP or non-polymorphic data
#' @param obj01Var States the variable which should be combined from the 
#' assayData slot. Default is intensity.
#' @param obj02Var States the variable which should be combined from the 
#' assayData slot. Default is intensity.
#' @param runtype Mode how the results are saved. Possible values are ff or bm. 
#' If ff is chosen the data will not be saved automatically. 
#' With bm the results will be saved permanently. 
#' @param saveFile Name of the file to save.
#' @return An instance of \code{\link[Biobase:class.ExpressionSet]{ExpressionSet}}.
#' @author Djork-Arne Clevert \email{okko@@clevert.de} and 
#' Andreas Mitterecker \email{mitterecker@@bioinf.jku.at}
#' @examples 
#' load(system.file("exampleData/normData.RData", package = "cn.farms"))
#' notes(experimentData(normData))$annotDir <- 
#'         system.file("exampleData/annotation/pd.genomewidesnp.6/1.1.0",
#'                 package = "cn.farms")
#' summaryMethod <- "Variational"
#' summaryParam <- list()
#' summaryParam$cyc <- c(10)
#' slData <- slSummarization(normData, 
#'         summaryMethod = summaryMethod, 
#'         summaryParam = summaryParam)
#' assayData(slData)$L_z[1:10, ] 
#' combData <- combineData(slData, slData)
#' combData
#' 
#' @export
combineData <- function (
        object01, 
        object02, 
        obj01Var = "intensity", 
        obj02Var = "intensity", 
        runtype  = "ff", 
        saveFile = "combData") {

    ## assure correct file extension
    saveFile <- gsub("\\.RData", "", saveFile)
    saveFile <- gsub("\\.rda", "", saveFile)
    saveFile <- paste(saveFile, ".RData", sep = "")
    
    if (runtype == "bm" & file.exists(saveFile)) {
        message("Combining the data has already been done")
        message("Trying to load combined data ...")
        load(saveFile)
        return(combData)
    }
    
    dataSnpType <- experimentData(object01)@other$type
    dataNpType <- experimentData(object02)@other$type
    
    colNamesSnp <- c("chrom", "start", "end", "man_fsetid")
    colNamesNp <-  c("chrom", "start", "end", "man_fsetid")
    
    if (dataSnpType == "slData" & dataNpType == "npData") {
        a <- fData(object01)[, colNamesSnp]
        b <- fData(object02)[, colNamesNp]
        colnames(b) <- colNamesSnp
    } else if (dataSnpType == "npData" & dataNpType == "slData") {
        a <- fData(object01)[, colNamesNp]
        b <- fData(object02)[, colNamesSnp]
        colnames(a) <- colNamesSnp
    } else if (dataSnpType == "slData" & dataNpType == "slData") {
        a <- fData(object01)[, colNamesSnp]
        b <- fData(object02)[, colNamesSnp]
    }  else if (dataSnpType == "npData" & dataNpType == "npData") {
        a <- fData(object01)[, colNamesNp]
        b <- fData(object02)[, colNamesNp]
    } else {
        stop("Wrong input objects")
    }
    
    phInfTmp <- rbind(a, b) 
    idx <- order(phInfTmp[, "chrom"], phInfTmp[, "start"])
    phInf <- phInfTmp[idx, ]
    rm(phInfTmp)
    cutoff <- nrow(a)
    nbrOfProbes <- nrow(phInf)
    nbrOfSamples <- ncol(assayData(object01)[[obj01Var]])
    
    
    intensity <- createMatrix(runtype, nbrOfProbes, nbrOfSamples, 
            type = "double", bmName = gsub("\\.RData", "", saveFile))
    
    intensity[which(idx <= cutoff), ] <- as.matrix(assayData(object01)[[obj01Var]][])
    intensity[which(idx > cutoff), ] <- as.matrix(assayData(object02)[[obj02Var]][])
    
    combData <- new("ExpressionSet")
    
    ## assay data    
    assayData(combData) <- list(intensity = intensity)
    
    ## protocol data
    protocolData(combData) <- protocolData(object01)
    
    ## pheno data
    phenoData(combData) <- phenoData(object01)
    
    ## feature data
    featureData(combData) <- new("AnnotatedDataFrame", 
            data = phInf)
    
    ## experiment data
    experimentData(combData) <- experimentData(object01)
    experimentData(combData)@other$type <- "combData"
    
    ## annotation
    ##annotation(combData) <- annotation(object01)
    
    if (runtype == "bm") {
        cat(paste(Sys.time(), "|   Saving normalized data \n"))
        save(combData, file = saveFile)
    }
    
    return(combData)
}