read.celfiles {oligo}R Documentation

Parser to CEL files

Description

Reads CEL files.

Usage

read.celfiles(..., filenames, pkgname, phenoData, featureData,
experimentData, notes, verbose = TRUE, sampleNames, rm.mask = FALSE,
rm.outliers = FALSE, rm.extra = FALSE, sd = FALSE, checkType = TRUE,
useAffyio = TRUE)

read.celfiles2(channel1, channel2, pkgname, phenoData, featureData,
experimentData, notes, verbose = TRUE, sampleNames, rm.mask = FALSE,
rm.outliers = FALSE, rm.extra = FALSE, sd = FALSE, checkType = TRUE,
useAffyio = 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
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?
sd logical. Read SD?
checkType logical. Check type of each file? This can be time consuming.
useAffyio logical. Use 'affyio' instead of 'affxparser' to read in CEL files.

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'.

Value

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

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)
}

[Package oligo version 1.8.3 Index]