createCel {affxparser}R Documentation

Creates an empty CEL file

Description

Creates an empty CEL file.

Usage

createCel(filename, header, nsubgrids=0, overwrite=FALSE, ..., 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().
overwrite If FALSE and the file already exists, an exception is thrown, otherwise the file is created.
nsubgrids The number of subgrids.
... Not used.
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 (http://www.braju.com/R/)

Examples

for (zzz in 0) {  # Only so that 'break' can be used

# Scan current directory for CEL files
outFile <- "zzz.CEL"
files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
files <- setdiff(files, outFile)
if (length(files) == 0)
  break

file <- files[1]

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read the CEL header
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
hdr <- readCelHeader(file)
if (hdr$version != 4)
  break

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Create a CEL v4 file of the same chip type
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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))

# Clean up
#rm(files, file, hdr, hdr2)
} # for (zzz in 0)

[Package affxparser version 1.8.3 Index]