applyCdfGroups {affxparser} | R Documentation

## Applies a function over the groups in a CDF structure

### Description

Applies a function over the groups in a CDF structure.

### Usage

    applyCdfGroups(cdf, fcn, ...)

### Arguments

`cdf` | A CDF `list` structure.
`fcn` | A `function` that takes a `list` structure of group elements and returns an updated `list` of groups.
`...` | Arguments passed to the `fcn` function.

### Value

Returns an updated CDF `list` structure.

### Pre-defined restructuring functions

- Generic:

  - `cdfGetFields`() - Gets a subset of groups fields in a CDF structure.

  - `cdfGetGroups`() - Gets a subset of groups in a CDF structure.

  - `cdfOrderBy`() - Orders the fields according to the value of another field in the same CDF group.

  - `cdfOrderColumnsBy`() - Orders the columns of fields according to the values in a certain row of another field in the same CDF group.

- Designed for SNP arrays:

  - `cdfAddBaseMmCounts`() - Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure.

  - `cdfAddProbeOffsets`() - Adds probe offsets to the groups in a CDF structure.

  - `cdfGtypeCelToPQ`() - Function to imitate Affymetrix' `gtype_cel_to_pq` software.

  - `cdfMergeAlleles`() - Function to join CDF allele A and allele B groups strand by strand.

  - `cdfMergeStrands`() - Function to join CDF groups with the same names.

We appreciate contributions.

### Author(s)

Henrik Bengtsson

### Examples

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

    cdfFile <- findCdf("Mapping10K_Xba131")

    # Identify the unit index from the unit name
    unitName <- "SNP_A-1509436"
    unit <- which(readCdfUnitNames(cdfFile) == unitName)

    # Read the CDF file
    cdf0 <- readCdfUnits(cdfFile, units=unit, stratifyBy="pmmm", readType=FALSE, readDirection=FALSE)
    cat("Default CDF structure:\n")
    print(cdf0)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Tabulate the information in each group
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    cdf <- readCdfUnits(cdfFile, units=unit)
    cdf <- applyCdfGroups(cdf, lapply, as.data.frame)
    print(cdf)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Infer the (true or the relative) offset for probe quartets.
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    cdf <- applyCdfGroups(cdf0, cdfAddProbeOffsets)
    cat("Probe offsets:\n")
    print(cdf)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Identify the number of nucleotides that mismatch the
    # allele A and the allele B sequences, respectively.
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    cdf <- applyCdfGroups(cdf, cdfAddBaseMmCounts)
    cat("Allele A & B target sequence mismatch counts:\n")
    print(cdf)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Combine the signals from  the sense and the anti-sense
    # strands in a SNP CEL files.
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # First, join the strands in the CDF structure.
    cdf <- applyCdfGroups(cdf, cdfMergeStrands)
    cat("Joined CDF structure:\n")
    print(cdf)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Rearrange values of group fields into quartets.  This
    # requires that the values are already arranged as PMs and MMs.
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    cdf <- applyCdfGroups(cdf0, cdfMergeAlleles)
    cat("Probe quartets:\n")
    print(cdf)

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Get the x and y cell locations (note, zero-based)
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    x <- unlist(applyCdfGroups(cdf, cdfGetFields, "x"), use.names=FALSE)
    y <- unlist(applyCdfGroups(cdf, cdfGetFields, "y"), use.names=FALSE)

    # Validate
    ncol <- readCdfHeader(cdfFile)$cols
    cells <- as.integer(y*ncol+x+1)
    cells <- sort(cells)

    cells0 <- readCdfCellIndices(cdfFile, units=unit)
    cells0 <- unlist(cells0, use.names=FALSE)
    cells0 <- sort(cells0)

    stopifnot(identical(cells0, cells))

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

[Package affxparser version 1.56.0 Index]