### Name: applyCdfGroups
### Title: Applies a function over the groups in a CDF structure
### Aliases: applyCdfGroups applyCdfBlocks
### Keywords: programming

### ** Examples

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

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}                                                     # STOP #
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