Read CEL files into an AffyBatch
Read CEL files into an Affybatch.
read.affybatch(..., filenames = character(0),
phenoData = new("AnnotatedDataFrame"),
description = NULL,
notes = "",
compress = getOption("BioC")$affy$compress.cel,
rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
verbose = FALSE,sd=FALSE, cdfname = NULL)
ReadAffy(..., filenames=character(0),
widget=getOption("BioC")$affy$use.widgets,
compress=getOption("BioC")$affy$compress.cel,
celfile.path=NULL,
sampleNames=NULL,
phenoData=NULL,
description=NULL,
notes="",
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE,
verbose=FALSE,sd=FALSE, cdfname = NULL)... |
file names separated by comma. |
filenames |
file names in a character vector. |
phenoData |
an |
description |
a |
notes |
notes. |
compress |
are the CEL files compressed? |
rm.mask |
should the spots marked as 'MASKS' set to |
rm.outliers |
should the spots marked as 'OUTLIERS' set to |
rm.extra |
if |
verbose |
verbosity flag. |
widget |
a logical specifying if widgets should be used. |
celfile.path |
a character denoting the path |
sampleNames |
a character vector of sample names to be used in
the |
sd |
should the standard deviation values in the CEL file be read in? Since these are typically not used default is not to read them in. This also save lots of memory. |
cdfname |
used to specify the name of an alternative cdf package.
If set to |
ReadAffy is a wrapper for read.affybatch that permits the
user to read in phenoData, MIAME information, and CEL files using
widgets. One can also define files where to read phenoData and MIAME
information.
If the function is called with no arguments ReadAffy() all the CEL
files in the working directory are read and put into an AffyBatch.
However, the arguments give the user great flexibility.
If phenoData is a character vector of length 1, the function
read.AnnotatedDataFrame is called to read a file
of that name and produce the AnnotationDataFrame object with the
sample metadata. If phenoData is a data.frame, it is
converted to an AnnotatedDataFrame.
If it is NULL and widget=FALSE (widget=TRUE is not currently
supported), then a default object of class
AnnotatedDataFrame is created,
whose pData is a data.frame with rownames being the names
of the CEL files, and with one column sample with an integer index.
AllButCelsForReadAffy is an internal function that gets called
by ReadAffy. It gets all the information except the cel intensities.
description is read using read.MIAME. If a
character is given, then it tries to read the file with that name to obtain a
MIAME instance. If left NULL but widget=TRUE, then
widgets are used. If left NULL and widget=FALSE, then an
empty instance of MIAME is created.
An AffyBatch object.
Ben Bolstad bmb@bmbolstad.com (read.affybatch), Laurent Gautier, and Rafael A. Irizarry (ReadAffy)
if(require(affydata)){
celpath <- system.file("celfiles", package="affydata")
fns <- list.celfiles(path=celpath,full.names=TRUE)
cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
##read a binary celfile
abatch <- ReadAffy(filenames=fns[1])
##read a text celfile
abatch <- ReadAffy(filenames=fns[2])
##read all files in that dir
abatch <- ReadAffy(celfile.path=celpath)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.