| File Parsers {oligo} | R Documentation |
Read Affymetrix CEL files into an FeatureSet.
read.celfiles(filenames,
pdenv=TRUE,
arrayType=NULL,
pkgname=NULL,
sd=FALSE,
npixels=FALSE,
phenoData=new("AnnotatedDataFrame"),
description=NULL,
notes="",
verbose=FALSE,
compress=FALSE,
rm.mask=FALSE,
rm.outliers=FALSE,
rm.extra=FALSE)
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)
filenames |
a character vector containing the file names. |
pdenv |
should load the standard Platform Design Environment (pdenv) associated to the CEL files? |
arrayType |
type of array: "SNP" or "expression". |
pkgname |
string specifying the alternative PDEnv to be loaded. (see Details) |
sd |
should return standard deviations? |
npixels |
should return number of pixels? |
phenoData |
a phenoData object. |
description |
a MIAME object. |
notes |
notes. |
verbose |
verbosity flag |
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 |
... |
extra arguments to be passed to list |
read.celfiles is an Affymetrix CEL file parser.
If pdenv is set to FALSE, then arrayType is required and
expected to assume either "SNP" or "expression". This will allow for
the correct assignment of the class of the object
(affysnpBatch/affyexprsBatch).
If pkgname is not NULL, then pdenv is
automatically set to FALSE.
The arguments pdenv, arrayType, pkgname and
uniquecdf are meant to be changed only by "power-users".
Either an affysnpBatch or an affyexprsBatch object,
depending on the type of the array (SNP or expression).
Benilton Carvalho bcarvalh@jhsph.edu, Rafael A. Irizarry, Ben Bolstad.
list.celfiles, read.xysfiles, list.xysfiles
## NOT RUN ## ## FeatureSet <- read.celfiles(list.celfiles())