QCIllumina-class        Class "QCIllumina"
RG2polar                Polar transformations
SnpSetIllumina          Class to Contain Objects Describing
                        High-Throughput SNP Assays.
alterCN                 alterCN
arrayType               Accessor methods for QC objects
backgroundCorrect.SNP   Background correction
backgroundEstimate      Estimate background intensities from foreground
                        intensity
calculateLOH            Determine LOH in experiment
calculateQCarray        Retrieve QC information from a SnpSetIllumina
                        object
chr17.260               Illumina example data
compareGenotypes        Compare genotypes
convert2aCGH            Conversion to Copynumber analysis objects
createCNSummary         Summarization of Copy number states
getDNAindex             Calculate the DNA index based on assigned copy
                        number values to probes
heterozygosity          Find regions of homozygous SNPs
heterozygousSNPs        Retrieve heterozygous SNPs
interactiveCNselect     Interactive assignment of copynumbers to
                        genomic segments
normalizeBetweenAlleles.SNP
                        between Allele normalization
normalizeLoci.SNP       locus normalization
normalizeWithinArrays.SNP
                        within Array normalization
pdfChromosomesSmoothCopyNumber
                        reportWrappers
pdfQC                   QCreport
plotGoldenGate4OPA      Plot Golden Gate genomic view
plotQC                  Spatial plots of array QC information
read.SnpSetIllumina     Read Experimental Data and into an
                        'SnpSetIllumina' Object
removeLowQualityProbes
                        Quality control of SnpSetIllumina objects
removeLowQualitySamples
                        Quality control of SnpSetIllumina objects
renameOPA               Change the linkage panel in a dataset
reportChromosomesSmoothCopyNumber
                        Genomic reports
reportGenotypeSegmentation
                        plot genomic view
reportSamplePanelQC-methods
                        reportSamplePanelQC
segmentate              Segmentation for SnpSetIllumina objects
setRealCN               Integrate state information into SNP object
smoothed.intensity      Smooth intensity data
standardNormalization   Default complete normalization
