read.xysfiles {oligo} | R Documentation

## Parser to XYS files

### Description

NimbleGen provides XYS files which are read by this function.

### Usage

    read.xysfiles(..., filenames, pkgname, phenoData, featureData,
    experimentData, notes, verbose=TRUE, sampleNames, checkType=TRUE)

    read.xysfiles2(channel1, channel2, pkgname, phenoData, featureData,
    experimentData, notes, verbose=TRUE, sampleNames, checkType=TRUE)

### Arguments

`...` | file names
`filenames` | `character` vector with 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` | `character` vector with alternative PD Info package name
`phenoData` | `phenoData`
`featureData` | `featureData`
`experimentData` | `experimentData`
`notes` | `notes`
`verbose` | `verbose`
`sampleNames` | `character` vector with sample names (usually better descriptors than the filenames)
`checkType` | `logical`. Check type of each file? This can be time consuming.

### Details

The function will read the XYS files provided by NimbleGen Systems and return an object of class FeatureSet.

### Value

``ExpressionFeatureSet`` | if Expresssion arrays
``TilingFeatureSet`` | if Tiling arrays

### See Also

`list.xysfiles`, `read.celfiles`

### Examples

    if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
    xysPath <- system.file("extdata", package="maqcExpression4plex")
    xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
    ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
    }

[Package oligo version 1.8.3 Index]