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| arrayID | Accessor methods for QC objects |
| arrayID,QCIllumina-method | Class "QCIllumina" |
| arrayID<-,QCIllumina-method | Class "QCIllumina" |
| arrayType | Accessor methods for QC objects |
| arrayType,QCIllumina-method | Class "QCIllumina" |
| arrayType<-,QCIllumina-method | Class "QCIllumina" |
| backgroundCorrect.SNP | Background correction |
| backgroundEstimate | Estimate background intensities from foreground intensity |
| calculateQCarray | Retrieve QC information from a SnpSetIllumina object |
| chr17.260 | Illumina example data |
| class:SnpSetIllumina | Class to Contain Objects Describing High-Throughput SNP Assays. |
| combine,SnpSetIllumina,ANY-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| combine,SnpSetIllumina,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| compareGenotypes | Compare genotypes |
| exprs,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| exprs<-,SnpSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| featureData,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| featureData<-,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| heterozygosity | Find regions of homozygous SNPs |
| heterozygousSNPs | Retrieve heterozygous SNPs |
| initialize,QCIllumina-method | Class "QCIllumina" |
| initialize,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| normalizeBetweenAlleles.SNP | between Allele normalization |
| normalizeLoci.SNP | locus normalization |
| normalizeWithinArrays.SNP | within Array normalization |
| pdfChromosomesSmoothCopyNumber | reportWrappers |
| pdfQC | QCreport |
| pdfSamplesSmoothCopyNumber | reportWrappers |
| plotQC | Spatial plots of array QC information |
| plotQC,QCIllumina-method | Class "QCIllumina" |
| polar2RG | Polar transformations |
| QC.260 | Illumina example data |
| QCIllumina-class | Class "QCIllumina" |
| read.SnpSetIllumina | Read Experimental Data and into an 'SnpSetIllumina' Object |
| removeLowQualityProbes | Quality control of SnpSetIllumina objects |
| removeLowQualitySamples | Quality control of SnpSetIllumina objects |
| reportChromosomesSmoothCopyNumber | Genomic reports |
| reporterInfo,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| reporterInfo<-,SnpSetIllumina,data.frame-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| reportSamplePanelQC | reportSamplePanelQC |
| reportSamplePanelQC,QCIllumina-method | reportSamplePanelQC |
| reportSamplePanelQC-methods | reportSamplePanelQC |
| reportSamplesSmoothCopyNumber | Genomic reports |
| RG2polar | Polar transformations |
| SnpSetIllumina | Class to Contain Objects Describing High-Throughput SNP Assays. |
| SnpSetIllumina-class | Class to Contain Objects Describing High-Throughput SNP Assays. |
| standardNormalization | Default complete normalization |
| [,SnpSetIllumina-method | Class to Contain Objects Describing High-Throughput SNP Assays. |