createCel: Creates an empty CEL file

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Creates an empty CEL file

Description

Creates an empty CEL file.

Usage

createCel(filename, header, nsubgrids=0, overwrite=FALSE, ..., cdf=NULL, verbose=FALSE)

Arguments

filename	The filename of the CEL file to be created.
header	A list structure describing the CEL header, similar to the structure returned by readCelHeader(). This header can be of any CEL header version.
overwrite	If FALSE and the file already exists, an exception is thrown, otherwise the file is created.
nsubgrids	The number of subgrids.
...	Not used.
cdf	(optional) The pathname of a CDF file for the CEL file to be created. If given, the CEL header (argument header) is validated against the CDF header, otherwise not. If TRUE, a CDF file is located automatically based using findCdf(header$chiptype).
verbose	An integer specifying how much verbose details are outputted.

Details

Currently only binary (v4) CEL files are supported. The current version of the method does not make use of the Fusion SDK, but its own code to create the CEL file.

Value

Returns (invisibly) the pathname of the file created.

Redundant fields in the CEL header

There are a few redundant fields in the CEL header. To make sure the CEL header is consistent, redundant fields are cleared and regenerated. For instance, the field for the total number of cells is calculated from the number of cell rows and columns.

Author(s)

Henrik Bengtsson

Examples

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

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


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read the CEL header
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
hdr <- readCelHeader(file)

# Assert that we found an ASCII CEL file, but any will do
stopifnot(hdr$version == 3)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Create a CEL v4 file of the same chip type
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
outFile <- file.path(tempdir(), "zzz.CEL")
if (file.exists(outFile))
  file.remove(outFile)
createCel(outFile, hdr, overwrite=TRUE)
str(readCelHeader(outFile))

# Verify correctness by update and re-read a few cells
intensities <- as.double(1:100)
indices <- seq(along=intensities)
updateCel(outFile, indices=indices, intensities=intensities)
value <- readCel(outFile, indices=indices)$intensities
stopifnot(identical(intensities, value))


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

HenrikBengtsson/affxparser documentation built on Nov. 10, 2024, 11:33 a.m.