| read.affybatch {affy} | R Documentation |
Read CEL files into an Affybatch
read.affybatch(..., filenames = character(0),
phenoData = new("phenoData"),
description = NULL,
notes = "",
compress = getOption("BioC")$affy$compress.cel,
rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE,
verbose = FALSE)
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)
... |
file names separated by comma. |
filenames |
file names in a character vector. |
phenoData |
a phenoData object |
description |
a MIAME object |
notes |
notes |
compress |
are the CEL files compressed ? |
rm.mask |
should the spots marked as 'MASKS' set to NA ? |
rm.outliers |
should the spots marked as 'OUTLIERS' set to NA |
rm.extra |
if TRUE, overrides what is in rm.mask and rm.oultiers |
verbose |
verbosity flag |
widget |
a logical specifying if widgets should be used. |
celfile.path |
a character denoting the path ReadAffy
should look for cel files |
sampleNames |
a character vector of sample names to be used in
the AffyBatch |
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 call 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.
phenoData is read using link[Biobase]{read.phenoData}. If a
character is given it tries to read the file with that name
to obtain the phenoData
object as described in link[Biobase]{read.phenoData}. If left
NULL but widget=TRUE then widgets are used. If left
NULL and widget=FALSE then a default object is created.
It will be a data frame with
new("phenoData",pData=data.frame(x=1:length(CELfiles)),varLabels=list(x="arbitrary number"))
AllButCelsForReadAffy is an internal function that gets called
by ReadAffy. It gets all the information expect the cel intencities.
description is read using read.MIAME. If a
character is given 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 bolstad@stat.berkeley.edu (read.affybatch), Laurent Gautier, and Rafael A. Irizarry (ReadAffy)
if(require(affydata)){
celpath <- paste(.path.package("affydata"),"celfiles",sep="/")
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)
}