File Parsers {oligo}R Documentation

Affymetrix CEL files parser

Description

Read Affymetrix CEL files into an FeatureSet.

Usage

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) 

Arguments

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

Details

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".

Value

Either an affysnpBatch or an affyexprsBatch object, depending on the type of the array (SNP or expression).

Author(s)

Benilton Carvalho bcarvalh@jhsph.edu, Rafael A. Irizarry, Ben Bolstad.

See Also

list.celfiles, read.xysfiles, list.xysfiles

Examples

## NOT RUN
##
## FeatureSet <- read.celfiles(list.celfiles())

[Package oligo version 0.99.15 Index]