| calculateQCarray {beadarraySNP} | R Documentation |
Retrieves QC and identifying information of Illumina Sentrix arrays.
calculateQCarray(object, QCobject = NULL, arrayType="Sentrix96")
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 |
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
A QCIllumina object, when multiple arrays were combined a list of QCIllumina objects
Jan Oosting
link{QCIllumina-class}, link{reportSamplePanelQC}, link{plotQC}
## Not run: QC<-calculateQCarray(data.raw1) ## Not run: QC<-calculateQCarray(data.raw2,QC)