QCIllumina-class: Class "QCIllumina"

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.