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())