read.affybatch {affy} | R Documentation |
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 |
a AnnotatedDataFrame 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 , then 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 . |
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
NULL , then the usual cdf package based on Affymetrix' mappings
will be used. |
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.
phenoData
is read using read.AnnotatedDataFrame
. If a
character is given it tries to read the file with that name
to obtain the AnnotationDataFrame
object as described in read.AnnotatedDataFrame
.
If left NULL
and widget=FALSE
(widget=TRUE
is not currently
supported), then a default object is created.
It will be an object of class AnnotatedDataFrame
with its pData being a data.frame with column x indexing the CEL files.
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) }