API for beadarraySNP
Normalization and reporting of Illumina SNP bead arrays

Global functions
.mergeAnnotateddata	Source code
.mergeAssayData	Source code
.mergefeatureData	Source code
BeadstudioQC	Man page Source code
GetBeadStudioSampleNames	Man page Source code
IlluminaGetGencalls	Source code
IlluminaGetOPAinfo	Source code
QC.260	Man page
QCIllumina	Man page
QCIllumina-class	Man page
RG2polar	Man page Source code
Sample_Map2Samplesheet	Man page Source code
SnpSetIllumina	Man page
SnpSetIllumina-class	Man page
SnpSetSegments-class	Man page
[,SnpSetIllumina-method	Man page
alterCN	Man page Source code
arrayID	Man page
arrayID,QCIllumina-method	Man page
arrayID<-	Man page
arrayID<-,QCIllumina-method	Man page
arrayType	Man page
arrayType,QCIllumina-method	Man page
arrayType<-	Man page
arrayType<-,QCIllumina-method	Man page
backgroundCorrect.SNP	Man page Source code
backgroundEstimate	Man page Source code
calculateGSR	Man page
calculateGSR,SnpSetIllumina-method	Man page
calculateLOH	Man page Source code
calculateLair	Man page Source code
calculateQCarray	Man page Source code
calculateSmooth	Man page
calculateSmooth,SnpSetIllumina,character-method	Man page
chr17.260	Man page
class:SnpSetIllumina	Man page
cn.segments	Man page
cn.segments,SnpSetSegments-method	Man page
cn.segments<-	Man page
cn.segments<-,SnpSetSegments,list-method	Man page
combine,SnpSetIllumina,ANY-method	Man page
combine,SnpSetIllumina,SnpSetIllumina-method	Man page
compareGenotypes	Man page Source code
convert2SegList	Man page Source code
convert2aCGH	Man page Source code
createCNSummary	Man page Source code
dist.GT	Man page Source code
exprs,SnpSetIllumina-method	Man page
exprs<-,SnpSetIllumina,matrix-method	Man page
fData,SnpSetIllumina-method	Man page
fData<-,SnpSetIllumina,data.frame-method	Man page
featureData,SnpSetIllumina-method	Man page
featureData<-,SnpSetIllumina-method	Man page
getAssayData	Source code
getDNAindex	Man page Source code
getExperiments	Source code
getGrouping	Source code
getMidMaxIdx	Source code
getNorTum	Source code
getSubsample	Source code
heterozygosity	Man page Source code
heterozygousSNPs	Man page Source code
initialize,QCIllumina-method	Man page
initialize,SnpSetIllumina-method	Man page
initialize,SnpSetSegments-method	Man page
interactiveCNselect	Man page Source code
normalizeBetweenAlleles.SNP	Man page Source code
normalizeBetweenSubsamples.SNP	Man page Source code
normalizeLoci.SNP	Man page Source code
normalizeWithinArrays.SNP	Man page Source code
pdfBeadstudioQC	Man page Source code
pdfChromosomeGainLossLOH	Man page Source code
pdfChromosomesSmoothCopyNumber	Man page Source code
pdfQC	Man page Source code
pdfSamplesSmoothCopyNumber	Man page Source code
plotGenomePanels	Man page Source code
plotGoldenGate4OPA	Man page Source code
plotGroupZygosity	Source code
plotQC	Man page
plotQC,QCIllumina-method	Man page
polar2RG	Man page Source code
read.SnpSetBeadstudio	Source code
read.SnpSetGencall	Source code
read.SnpSetIllumina	Man page Source code
read.SnpSetSampleSheet	Source code
readClusteringData	Source code
readReportfile	Source code
removeLowQualityProbes	Man page Source code
removeLowQualitySamples	Man page Source code
renameOPA	Man page Source code
reportChromosomeGainLossLOH	Man page Source code
reportChromosomesSmoothCopyNumber	Man page Source code
reportGenomeGainLossLOH	Man page Source code
reportGenomeIntensityPlot	Man page Source code
reportGenotypeSegmentation	Man page Source code
reportSamplePanelQC	Man page
reportSamplePanelQC,QCIllumina-method	Man page
reportSamplePanelQC-methods	Man page
reportSamplesSmoothCopyNumber	Man page Source code
segmentate	Man page Source code
segmentate.old	Source code
setRealCN	Man page Source code
smoothed.intensity	Man page Source code
smoothed.probes	Source code
smoothed.size	Source code
sortGenomic	Man page
sortGenomic,SnpSetIllumina-method	Man page
standardNormalization	Man page Source code