parseSourceFile {VanillaICE} | R Documentation

## Function for parsing GenomeStudio files

### Description

This function parses genome studio files, writing the low-level data for log R ratios, B allele frequencies, and genotypes to disk as integers (1 file per subject per data type).

### Usage

    parseSourceFile(object, param)

    ## S4 method for signature 'ArrayViews,CopyNumScanParams'
    parseSourceFile(object, param)

### Arguments

`object` | An `ArrayViews` object
`param` | An object of class `CopyNumScanParams`

### See Also

`ArrayViews` `ArrayViews` `CopyNumScanParams`

### Examples

      require(BSgenome.Hsapiens.UCSC.hg18)
      bsgenome <- BSgenome.Hsapiens.UCSC.hg18
      require(data.table)
      extdir <- system.file("extdata", package="VanillaICE", mustWork=TRUE)
      features <- suppressWarnings(fread(file.path(extdir, "SNP_info.csv")))
      fgr <- GRanges(paste0("chr", features$Chr), IRanges(features$Position, width=1),
                     isSnp=features[["Intensity Only"]]==0)
      fgr <- SnpGRanges(fgr)
      names(fgr) <- features[["Name"]]
      seqlevels(fgr) <- seqlevels(bsgenome)[seqlevels(bsgenome) %in% seqlevels(fgr)]
      seqinfo(fgr) <- seqinfo(bsgenome)[seqlevels(fgr),]
      fgr <- sort(fgr)
      files <- list.files(extdir, full.names=TRUE, recursive=TRUE, pattern="FinalReport")
      views <- ArrayViews(rowRanges=fgr, sourcePaths=files, parsedPath=tempdir())
      show(views)

    ## read the first file
    dat <- fread(files[1], skip="[Data]")
    ## information to store on the markers
    select <- match(c("SNP Name", "Allele1 - AB", "Allele2 - AB",
                      "Log R Ratio", "B Allele Freq"), names(dat))
    ##
    ## which rows to keep in the MAP file. By matching on the sorted GRanges object
    ## containing the feature annotation, the low-level data for the log R ratios/
    ## B allele frequencies will also be sorted
    ##
    index_genome <- match(names(fgr), dat[["SNP Name"]])
    scan_params <- CopyNumScanParams(index_genome=index_genome, select=select)
    ##
    ## parse the source files
    ##
    parseSourceFile(views, scan_params)
    list.files(parsedPath(views))
    ##
    ##  Inspecting source data through accessors defined on the views object
    ##
    require(oligoClasses)
    ## log R ratios
    r <- head(lrr(views))
    ## B allele frequencies
    b <- head(baf(views))
    g <- head(genotypes(views))

[Package VanillaICE version 1.46.0 Index]