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.

Value

A QCIllumina object

Author(s)

Jan Oosting

See Also

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

Examples

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

[Package beadarraySNP version 1.6.0 Index]