updateCelUnits: Updates a CEL file unit by unit

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Updates a CEL file unit by unit

Description

Updates a CEL file unit by unit.

Please note that, contrary to readCelUnits(), this method can only update a single CEL file at the time.

Usage

updateCelUnits(filename, cdf=NULL, data, ..., verbose=0)

Arguments

filename	The filename of the CEL file.
cdf	A (optional) CDF list structure either with field indices or fields x and y. If NULL, the unit names (and from there the cell indices) are inferred from the names of the elements in data.
data	A list structure in a format similar to what is returned by readCelUnits() for a single CEL file only.
...	Optional arguments passed to readCdfCellIndices(), which is called if cdf is not given.
verbose	An integer specifying how much verbose details are outputted.

Value

Returns what updateCel() returns.

Working with re-arranged CDF structures

Note that if the cdf structure is specified the CDF file is not queried, but all information about cell x and y locations, that is, cell indices is expected to be in this structure. This can be very useful when one work with a cdf structure that originates from the underlying CDF file, but has been restructured for instance through the applyCdfGroups() method, and data correspondingly. This update method knows how to update such structures too.

Author(s)

Henrik Bengtsson

See Also

Internally, updateCel() is used.

Examples

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

# Search for some available Calvin CEL files
path <- system.file("rawData", package="AffymetrixDataTestFiles")
files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE)
files <- grep("FusionSDK_Test3", files, value=TRUE)
files <- grep("Calvin", files, value=TRUE)
file <- files[1]

# Convert to an XDA CEL file
pathname <- file.path(tempdir(), basename(file))
if (file.exists(pathname))
  file.remove(pathname)
convertCel(file, pathname)




# Check for the CDF file
hdr <- readCelHeader(pathname)
cdfFile <- findCdf(hdr$chiptype)

hdr <- readCdfHeader(cdfFile)
nbrOfUnits <- hdr$nunits
print(nbrOfUnits);

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Read and re-write the same data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
units <- c(101, 51)
data1 <- readCelUnits(pathname, units=units, readStdvs=TRUE)
cat("Original data:\n")
str(data1)
updateCelUnits(pathname, data=data1)
data2 <- readCelUnits(pathname, units=units, readStdvs=TRUE)
cat("Updated data:\n")
str(data2)
stopifnot(identical(data1, data2))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Random read and re-write "stress test"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for (kk in 1:10) {
  nunits <- sample(min(1000,nbrOfUnits), size=1)
  units <- sample(nbrOfUnits, size=nunits)
  cat(sprintf("%02d. Selected %d random units: reading", kk, nunits));
  t <- system.time({
    data1 <- readCelUnits(pathname, units=units, readStdvs=TRUE)
  }, gcFirst=TRUE)[3]
  cat(sprintf(" [%.2fs=%.2fs/unit], updating", t, t/nunits))
  t <- system.time({
    updateCelUnits(pathname, data=data1)
  }, gcFirst=TRUE)[3]
  cat(sprintf(" [%.2fs=%.2fs/unit], validating", t, t/nunits))
  data2 <- readCelUnits(pathname, units=units, readStdvs=TRUE)
  stopifnot(identical(data1, data2))
  cat(". done\n")
}

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

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.