readCel(filename, indices = NULL, readHeader = TRUE, readXY = FALSE, readIntensities = TRUE, readStdvs = FALSE, readPixels = FALSE, readOutliers = TRUE, readMasked = TRUE, readMap = NULL, verbose = 0, .checkArgs = TRUE)
NULL
all features will be returned.TRUE
, the arguments will be validated,
otherwise not. Warning: This should only be used if the
arguments have been validated elsewhere!masked
cells.The cell values, which are values extract for each cell (aka feature
or probe), are the (x,y) coordinate, intensity and standard deviation
estimates, and the number of pixels in the cell.
If readIndices=NULL
, cell values for all cells are returned,
Only cell values specified by argument readIndices
are returned.This value returns a named list with compontents described below:header
readCelHeader
, see the documentation for that
function.integer
vectors containing
the x and y coordinates associated with each feature.intensities
numeric
vector
containing the intensity associated with each feature.numeric
vector containing
the standard deviation associated with each feature.integer
vector containing
the number of pixels associated with each feature.integer
vector of indices specifying which
of the queried cells that are flagged as outliers.
Note that there is a difference between outliers=NULL
and
outliers=integer(0)
; the last case happens when
readOutliers=TRUE
but there are no outliers.integer
vector of indices specifying which
of the queried cells that are flagged as masked.
Note that there is a difference between masked=NULL
and
masked=integer(0)
; the last case happens when
readMasked=TRUE
but there are no masked features.indices
. The lengths of the cell-value elements equals the
number of cells read.Which of the above elements that are returned are controlled by the
readNnn
arguments. If FALSE
, the corresponding element
above is NULL
, e.g. if readStdvs=FALSE
then
stdvs
is NULL
.
indices
argument will therefore
only affect the memory use of the final object (as well as speed), not
the memory allocated in the C function used to parse the file. This
should be a minor problem however.readCelHeader()
for a description of the header output.
Often a user only wants to read the intensities, look at
readCelIntensities()
for a function specialized for
that use.
for (zzz in 0) { # Only so that 'break' can be used
# Scan current directory for CEL files
celFiles <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
if (length(celFiles) == 0)
break;
celFile <- celFiles[1]
# Read a subset of cells
idxs <- c(1:5, 1250:1500, 450:440)
cel <- readCel(celFile, indices=idxs, readOutliers=TRUE)
str(cel)
# Clean up
rm(celFiles, celFile, cel)
} # for (zzz in 0)
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