calculateQCarray {beadarraySNP} | R Documentation

## Retrieve QC information from a SnpSetIllumina object

### Description

Retrieves QC and identifying information of Illumina Sentrix arrays.

### Usage

    calculateQCarray(object, QCobject = NULL, arrayType="Sentrix96")

### Arguments

`object` | `SnpSetIllumina` object. Should contain information of a single Sentrix array and a single type of OPA panel
`QCobject` | `QCIllumina-class` object: If set the information in the object is amended with data from the SnpSetIllumina object
`arrayType` | character, see `arrayType`

### Details

Sample summary values are mapped to the physical layout of the Sentrix array using the `Row` and `Col` columns of the `phenoData` slot. These will be available when `read.SnpSetIllumina` is used to create `SnpSetIllumina` objects.
Use successive calls to `calculateQCarray` to process Sentrix arrays with multiple probe panels.

If data is read using a samplesheet that defines manifest files it is possible to handle data with multiple manifests and/or multiple Sentrix arrays

### Value

A `QCIllumina` object, when multiple arrays were combined a list of `QCIllumina` objects

### Author(s)

Jan Oosting

### See Also

`link{QCIllumina-class}`, `link{reportSamplePanelQC}`, `link{plotQC}`

### Examples

      ## Not run: QC<-calculateQCarray(data.raw1)
      ## Not run: QC<-calculateQCarray(data.raw2,QC)

[Package beadarraySNP version 1.52.0 Index]