QCIllumina-class {beadarraySNP} | R Documentation

## Class "QCIllumina"

### Description

Container of QC information on arrays that contain multiple samples.

### Objects from the Class

Objects can be created by calls of the form `new("QCIllumina", arrayType, arrayID, intensityMed, greenMed, redMed, intensityMode, greenMode, redMode, validn, annotation, samples)`, but are usually created by `calculateQCarray`.

### Slots

`arrayType`:

  character, Type of array. See `arrayType`

`arrayID`:

  character, Array ID

`intensityMed`:

  numeric matrix, Median of intensity of samples

`greenMed`:

  numeric matrix, Median of green values

`redMed`:

  numeric matrix, Median of red values

`callrate`:

  numeric matrix, callrate of genotyping

`hetPerc`:

  numeric matrix, Percentage of heterozygotes

`ptpdiff`:

  numeric matrix, point-to-point difference, local estimate of variability

`validn`:

  numeric matrix, Number of valid probe values in samples

`annotation`:

  character matrix, Annotation of samples

`samples`:

  character matrix, Sample IDs

### Methods

arrayID

  `signature(object = "QCIllumina")`: Returns type of array

arrayID<-

  `signature(object = "QCIllumina")`: Sets type of array. Currently only `"Sentrix"` is supported

arrayType

  `signature(object = "QCIllumina")`: Returns ID of array

arrayType<-

  `signature(object = "QCIllumina")`: Sets ID/Barcode of array

initialize

  `signature(.Object = "QCIllumina")`

plotQC

  `signature(object = "QCIllumina")``character`: plots spatial overview of QC information, `type` is one of `c("intensityMed", "greenMed","redMed","validn","annotation","samples")`

### Author(s)

Jan Oosting

### See Also

`calculateQCarray`

[Package beadarraySNP version 1.53.0 Index]