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
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 1.8.0 Index]