oligo (version 1.36.1)

read.celfiles: Parser to CEL files

Description

Reads CEL files.

Usage

read.celfiles(..., filenames, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, checkType=TRUE)
read.celfiles2(channel1, channel2, pkgname, phenoData, featureData,
experimentData, protocolData, notes, verbose=TRUE, sampleNames,
rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, checkType=TRUE)

Arguments

...

names of files to be read.

filenames

a character vector with the CEL filenames.

channel1

a character vector with the CEL filenames for the first 'channel' on a Tiling application

channel2

a character vector with the CEL filenames for the second 'channel' on a Tiling application

pkgname

alternative data package to be loaded.

phenoData

phenoData

featureData

featureData

experimentData

experimentData

protocolData

protocolData

notes

notes

verbose

logical

sampleNames

character vector with sample names (usually better descriptors than the filenames)

rm.mask

logical. Read masked?

rm.outliers

logical. Remove outliers?

rm.extra

logical. Remove extra?

checkType

logical. Check type of each file? This can be time consuming.

Value

• ExpressionFeatureSet
  if Expresssion arrays
• ExonFeatureSet
  if Exon arrays
• SnpFeatureSet
  if SNP arrays
• TilingFeatureSet
  if Tiling arrays

Details

When using 'affyio' to read in CEL files, the user can read compressed CEL files (CEL.gz). Additionally, 'affyio' is much faster than 'affxparser'.

The function guesses which annotation package to use from the header of the CEL file. The user can also provide the name of the annotaion package to be used (via the pkgname argument). If the annotation package cannot be loaded, the function returns an error. If the annotation package is not available from BioConductor, one can use the pdInfoBuilder package to build one.

See Also

list.celfiles, read.xysfiles

Examples

if(require(pd.mapping50k.xba240) & require(hapmap100kxba)){
celPath <- system.file("celFiles", package="hapmap100kxba")
celFiles <- list.celfiles(celPath, full.name=TRUE)
affySnpFeatureSet <- read.celfiles(celFiles)
}