calculateQCarray: Retrieve QC information from a SnpSetIllumina object

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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.

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

Value

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

Author(s)

Jan Oosting

See Also

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

Examples

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

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