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:
Object of class "character" Type of array. Currently restricted to "Sentrix"
arrayID:
Object of class "character" Array ID
intensityMed:
Object of class "matrix" Median of intensity of samples
greenMed:
Object of class "matrix" Median of green values
redMed:
Object of class "matrix" Median of red values
validn:
Object of class "matrix" Number of valid probe values in samples
annotation:
Object of class "matrix" Annotation of samples
samples:
Object of class "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 1.0.0 Index]