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]