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=getwd(), 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"))
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) }