readCdfUnitsWriteMap {affxparser} | R Documentation

## Generates an Affymetrix cell-index write map from a CDF file

### Description

Generates an Affymetrix cell-index write map from a CDF file.

The purpose of this method is to provide a re-ordering of cell elements such that cells in units (probesets) can be stored in contigous blocks. When reading cell elements unit by unit, minimal file re-position is required resulting in a faster reading.

Note: At the moment does this package not provide methods to write/reorder CEL files. In the meanwhile, you have to write and re-read using your own file format. That's not too hard using `writeBin()` and `readBin`().

### Usage

    readCdfUnitsWriteMap(filename, units=NULL, ..., verbose=FALSE)

### Arguments

`filename` | The pathname of the CDF file.
`units` | An `integer` `vector` of unit indices specifying which units to listed first. All other units are added in order at the end. If `NULL`, units are in order.
`...` | Additional arguments passed to `readCdfUnits`().
`verbose` | Either a `logical`, a `numeric`, or a `Verbose` object specifying how much verbose/debug information is written to standard output. If a Verbose object, how detailed the information is is specified by the threshold level of the object. If a numeric, the value is used to set the threshold of a new Verbose object. If `TRUE`, the threshold is set to -1 (minimal). If `FALSE`, no output is written (and neither is the R.utils package required).

### Value

A `integer` `vector` which is a write map.

### Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

### See Also

To invert maps, see `invertMap`(). `readCel`() and `readCelUnits`().

### Examples

       ##############################################################
    if (require("AffymetrixDataTestFiles")) {            # START #
    ##############################################################

    # Find any CDF file
    cdfFile <- findCdf()

    # Create a cell-index map (for writing)
    writeMap <- readCdfUnitsWriteMap(cdfFile)

    # Inverse map to be used to read cell elements such that, when read
    # read unit by unit, they are read much faster.
    readMap <- invertMap(writeMap)

    # Validate the two maps
    stopifnot(identical(readMap[writeMap], 1:length(readMap)))

    cat("Summary of the \"randomness\" of the cell indices:\n")
    moves <- diff(readMap) - 1
    cat(sprintf("Number of unnecessary file re-positioning: %d (%.1f%%)\n",
                       sum(moves != 0), 100*sum(moves != 0)/length(moves)))
    cat(sprintf("Extra positioning: %.1fGb\n", sum(abs(moves))/1024^3))

    smallMoves <- moves[abs(moves) <= 25];
    largeMoves <- moves[abs(moves)  > 25];
    layout(matrix(1:2))
    main <- "Non-signed file moves required in unorded file"
    hist(smallMoves, nclass=51, main=main, xlab="moves <=25 bytes")
    hist(largeMoves, nclass=101, main="", xlab="moves >25 bytes")

    # Clean up
    layout(1)
    rm(cdfFile, readMap, writeMap, moves, smallMoves, largeMoves, main)

    ##############################################################
    }                                                     # STOP #
    ##############################################################

       ##############################################################
    if (require("AffymetrixDataTestFiles")) {            # START #
    ##############################################################

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Function to read Affymetrix probeset annotations
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    readAffymetrixProbesetAnnotation <- function(pathname, ...) {
      # Get headers
      header <- scan(pathname, what="character", sep=",", quote="\"",
                                                          quiet=TRUE, nlines=1);

      # Read only a subset of columns (unique to this example)
      cols <- c("Probe Set ID"="probeSet",
                "Chromosome"="chromosome",
                "Physical Position"="physicalPosition",
                "dbSNP RS ID"="dbSnpId");

      colClasses <- rep("NULL", length(header));
      colClasses[header %in% names(cols)] <- "character";

      # Read the data (this is what takes time)
      df <- read.table(pathname, colClasses=colClasses, header=TRUE, sep=",",
             quote="\"", na.strings="---", strip.white=TRUE, check.names=FALSE,
                     blank.lines.skip=FALSE, fill=FALSE, comment.char="", ...);

      # Re-order columns
      df <- df[,match(names(cols),colnames(df))];
      colnames(df) <- cols;

      # Use "Probe Set ID" as rownames. Note that if we use 'row.names=1'
      # or similar something goes wrong. /HB 2006-03-06
      rownames(df) <- df[[1]];
      df <- df[,-1];

      # Change types of columns
      df[[1]] <- factor(df[[1]], levels=c(1:22,"X","Y",NA), ordered=TRUE);
      df[[2]] <- as.integer(df[[2]]);

      df;
    } # readAffymetrixProbesetAnnotation()

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Main
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    for (zz in 1) {
    # Chip to be remapped
    chipType <- "Mapping50K_Xba240"

    annoFile <- paste(chipType, "_annot.csv", sep="")
    cdfFile <- findCdf(chipType)
    if (is.null(cdfFile) || !file.exists(annoFile))
      break;

    # Read SNP location details
    snpInfo <- readAffymetrixProbesetAnnotation(annoFile)

    # Order by chromsome and then physical position
    o <- order(snpInfo[[1]], snpInfo[[2]])
    snpInfo <- snpInfo[o,]
    rm(o)

    # Read unit names in CDF file
    unitNames <- readCdfUnitNames(cdfFile)

    # The CDF unit indices sorted by chromsomal position
    units <- match(rownames(snpInfo), unitNames)

    # ...and cell indices in the same order
    writeMap <- readCdfUnitsWriteMap(cdfFile, units=units)

    # Inverse map to be used to write cell elements such that, if they
    # later are read unit by unit, they are read in contiguous blocks.
    readMap <- invertMap(writeMap)

    # Clean up
    rm(chipType, annoFile, cdfFile, snpInfo, unitNames, units, readMap, writeMap)

    } # for (zz in 1)
    ##############################################################
    }                                                     # STOP #
    ##############################################################

[Package affxparser version 1.16.0 Index]