read.celfiles {oligo} | R Documentation

## 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.

### 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.

### 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 1.54.1 Index]