R/buildData.R

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

################################
## Build a Agilent object
################################
readAgilent <- function(filePath, sampleName = NA, labName = NA,
    supFlags = TRUE, genome = c("hg19", "hg18", "hg38"),
    ploidy = 2, verbose = TRUE){

    if(!.validAgilent(filePath))
        return(NULL)

    fileName <- gsub("(.*)/", "", filePath)
    genome <- match.arg(genome)
    object <- new(
        "rCGH-Agilent",
        info = c(fileName=fileName, sampleName=sampleName, labName=labName,
            analysisDate = format(Sys.Date(), "%Y-%m-%d"),
            platform='Agilent', suppressFlags=supFlags,
            genome = genome, ploidy = ploidy)
        )
    object@info <- c(object@info, .readAgilentInfo(filePath, verbose))
    object@cnSet <- .readAgilentMatrix(filePath, verbose)

    if(supFlags){
        object <- .suppressFlags(object, verbose)
    }

    object <- .suppressDuplic(object, verbose)
    object <- .preset(object)
    setInfo(object, "rCGH_version") <- as.character(packageVersion("rCGH"))

#    .createGeneDB(genome)

    if(verbose)
        message("Genome build: ", genome)

    return (object)
}

############################
## Build a SNP6 object
############################
readAffySNP6 <- function(filePath, sampleName = NA, labName = NA,
    useProbes = c("snp", "cn", "all"), genome = c("hg19", "hg18", "hg38"),
    ploidy = 2, verbose = TRUE){

    if(!.validSNP6(filePath))
        return(NULL)
    
    useProbes <- match.arg(useProbes)
    genome <- match.arg(genome)

    if(verbose)
        message(toupper(useProbes), " probes will be used.")

    fileName <- gsub("(.*)/", "", filePath)
    object <- new(
        "rCGH-SNP6",
        info = c(fileName=fileName, sampleName=sampleName, labName=labName,
            analysisDate = format(Sys.Date(), "%Y-%m-%d"),
            usedProbes = useProbes, genome = genome,
            ploidy = ploidy)
        )

    affyData <- .readSNP6(filePath, useProbes, verbose)
    object@info <- c(object@info, affyData$infos)
    object@cnSet <- affyData$cnSet

    if(verbose)
        message("Adding presettings...")

    object <- .preset(object)
    setInfo(object, "rCGH_version") <- as.character(packageVersion("rCGH"))

#    .createGeneDB(genome)

    if(verbose)
        message("Genome build: ", genome)

    return (object)
}

################################
## Build a AffyCytoScan object
################################

readAffyCytoScan <- function(filePath, sampleName = NA, labName = NA, 
    useProbes = c("snp", "cn", "all"), genome = c("hg19", "hg18", "hg38"),
    ploidy = 2, verbose = TRUE){

    if(!.validCytoScan(filePath))
        return(NULL)

    useProbes <- match.arg(useProbes)
    genome <- match.arg(genome)

    if(verbose)
        message(toupper(useProbes), " probes will be used.")

    fileName <- gsub("(.*)/", "", filePath)
    object <- new(
        "rCGH-cytoScan",
        info = c(fileName=fileName, sampleName=sampleName, labName=labName,
            analysisDate = format(Sys.Date(), "%Y-%m-%d"),
            usedProbes = useProbes, genome = genome,
            ploidy = ploidy)
        )

    affyData <- .readCytoScan(filePath, useProbes, verbose)
    object@info <- c(object@info, affyData$infos)
    object@cnSet <- affyData$cnSet

    if(verbose) 
        message("Adding presettings...")

    object <- .preset(object)
    setInfo(object, "rCGH_version") <- as.character(packageVersion("rCGH"))

#    .createGeneDB(genome)

    if(verbose)
        message("Genome build: ", genome)

    return (object)
}

################################
## Build a Affy OncoScan object
################################
readAffyOncoScan <- function(filePath, sampleName = NA, labName = NA,
    genome = c("hg19", "hg18", "hg38"), ploidy = 2, verbose = TRUE){

    genome <- match.arg(genome)

    fileName <- gsub("(.*)/", "", filePath)

    object <- new(
        "rCGH-oncoScan",
        info = c(fileName=fileName, sampleName=sampleName, labName=labName,
            analysisDate = format(Sys.Date(), "%Y-%m-%d"),
            usedProbes = NA, genome = genome,
            platform = "OncoScan", ploidy = ploidy)
        )

    cnSet <- read.delim(filePath, stringsAsFactors = FALSE)
    colnames(cnSet)[1:3] <- c("ProbeName", "ChrNum", "ChrStart")
    idx <- grep("AllelicDifference", colnames(cnSet))
    if(length(idx) == 1)
        colnames(cnSet)[idx] <- "Allele.Difference"
    cnSet$ChrNum <- .renameChr(cnSet$ChrNum)

    object@cnSet <- cnSet[order(cnSet$ChrNum, cnSet$ChrStart),]

    if(verbose)
        message("Adding presettings...")

    object <- .preset(object)
    setInfo(object, "rCGH_version") <- as.character(packageVersion("rCGH"))

    if(verbose)
        message("Genome build: ", genome)

    return (object)
}

################################
## Build a generic object
################################
readGeneric <- function(filePath, sampleName=NA, labName=NA,
    genome = c("hg19", "hg18", "hg38"), ploidy = 2, verbose=TRUE){

    fileName <- gsub("(.*)/", "", filePath)
    genome <- match.arg(genome)
    object <- new(
        "rCGH-generic",
        info = c(fileName=fileName, sampleName=sampleName, labName=labName,
                analysisDate = format(Sys.Date(), "%Y-%m-%d"),
                usedProbes = NA, genome = genome,
                ploidy = ploidy)
    )
    
    object@cnSet <- .readGeneric(filePath)

    if(verbose) 
        message("Adding presettings...")

    object <- .preset(object)
    setInfo(object, "rCGH_version") <- as.character(packageVersion("rCGH"))
    
#    .createGeneDB(genome)

    if(verbose)
        message("Genome build: ", genome)

    return(object)
}