beadarraySNP (version 1.38.0)

calculateQCarray: 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

Value

A QCIllumina object, when multiple arrays were combined a list of QCIllumina objects

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. If data is read using a samplesheet that defines manifest files it is possible to handle data with multiple manifests and/or multiple Sentrix arrays

See Also

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

Examples

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