read.affybatch {affy}R Documentation

Read CEL files into an AffyBatch

Description

Read CEL files into an Affybatch

Usage

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=NULL,
              sampleNames=NULL,
              phenoData=NULL,
              description=NULL,
              notes="",
              rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE,
              verbose=FALSE)

Arguments

... 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

Details

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"))

AllButCelsForReadAffy is an internal function that gets called by ReadAffy. It gets all the information expect the cel intencities.

description is read using read.MIAME. If a character is given 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..

Value

An AffyBatch object.

Author(s)

Ben Bolstad bolstad@stat.berkeley.edu (read.affybatch), Laurent Gautier, and Rafael A. Irizarry (ReadAffy)

See Also

AffyBatch

Examples

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)
}

[Package affy version 1.8.1 Index]