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| alterCN | alterCN |
| arrayID | Accessor methods for QC objects |
| arrayID-method | Class "QCIllumina" |
| arrayID<- | Accessor methods for QC objects |
| arrayID<--method | Class "QCIllumina" |
| arrayType | Accessor methods for QC objects |
| arrayType-method | Class "QCIllumina" |
| arrayType<- | Accessor methods for QC objects |
| arrayType<--method | Class "QCIllumina" |
| backgroundCorrect.SNP | Background correction |
| backgroundEstimate | Estimate background intensities from foreground intensity |
| BeadstudioQC | Quality control of Beadstudio report files |
| calculateGSR | Class to Contain Objects Describing High-Throughput SNP Assays. |
| calculateGSR-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| calculateLair | Determine LOH in experiment |
| calculateLOH | Determine LOH in experiment |
| calculateQCarray | Retrieve QC information from a SnpSetIllumina object |
| calculateSmooth | Class to Contain Objects Describing High-Throughput SNP Assays. |
| calculateSmooth-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| chr17.260 | Illumina example data |
| class:SnpSetIllumina | Class to Contain Objects Describing High-Throughput SNP Assays. |
| cn.segments | Class "SnpSetSegments" |
| cn.segments-method | Class "SnpSetSegments" |
| cn.segments<- | Class "SnpSetSegments" |
| cn.segments<--method | Class "SnpSetSegments" |
| combine-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| compareGenotypes | Compare genotypes |
| convert2aCGH | Conversion to Copynumber analysis objects |
| convert2SegList | Conversion to Copynumber analysis objects |
| createCNSummary | Summarization of Copy number states |
| dist.GT | dist.GT |
| exprs-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| exprs<--method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| fData-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| fData<--method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| featureData-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| featureData<--method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| GetBeadStudioSampleNames | Extract samplenames from a report file |
| getDNAindex | Calculate the DNA index based on assigned copy number values to probes |
| heterozygosity | Find regions of homozygous SNPs |
| heterozygousSNPs | Retrieve heterozygous SNPs |
| initialize-method | Class "QCIllumina" |
| initialize-method | Class "SnpSetSegments" |
| initialize-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| interactiveCNselect | Interactive assignment of copynumbers to genomic segments |
| normalizeBetweenAlleles.SNP | between Allele normalization |
| normalizeBetweenSubsamples.SNP | Normalization between subsamples |
| normalizeLoci.SNP | locus normalization |
| normalizeWithinArrays.SNP | Within Array normalization |
| pdfBeadstudioQC | Quality control of Beadstudio report files |
| pdfChromosomeGainLossLOH | reportWrappers |
| pdfChromosomesSmoothCopyNumber | reportWrappers |
| pdfQC | QCreport |
| pdfSamplesSmoothCopyNumber | reportWrappers |
| plotGenomePanels | Plot Golden Gate genomic view |
| plotGoldenGate4OPA | Plot Golden Gate genomic view |
| plotQC | Spatial plots of array QC information |
| plotQC-method | Class "QCIllumina" |
| polar2RG | Polar transformations |
| QC.260 | Illumina example data |
| QCIllumina | Class "QCIllumina" |
| QCIllumina-class | Class "QCIllumina" |
| read.SnpSetIllumina | Read Experimental Data, Featuredata and Phenodata into an 'SnpSetIllumina' Object |
| removeLowQualityProbes | Quality control of SnpSetIllumina objects |
| removeLowQualitySamples | Quality control of SnpSetIllumina objects |
| renameOPA | Change the linkage panel in a dataset |
| reportChromosomeGainLossLOH | Genomic reports |
| reportChromosomesSmoothCopyNumber | Genomic reports |
| reportGenomeGainLossLOH | Genomic reports |
| reportGenomeIntensityPlot | Genomic reports |
| reportGenotypeSegmentation | plot genomic view |
| reportSamplePanelQC | reportSamplePanelQC |
| reportSamplePanelQC-method | reportSamplePanelQC |
| reportSamplePanelQC-methods | reportSamplePanelQC |
| reportSamplesSmoothCopyNumber | Genomic reports |
| RG2polar | Polar transformations |
| Sample_Map2Samplesheet | Convert Beadstudio Sample Map file to samplesheet |
| segmentate | Segmentation for SnpSetIllumina objects |
| setRealCN | Integrate state information into SNP object |
| smoothed.intensity | Smooth intensity data |
| SnpSetIllumina | Class to Contain Objects Describing High-Throughput SNP Assays. |
| SnpSetIllumina-class | Class to Contain Objects Describing High-Throughput SNP Assays. |
| SnpSetSegments-class | Class "SnpSetSegments" |
| sortGenomic | Class to Contain Objects Describing High-Throughput SNP Assays. |
| sortGenomic-method | Class to Contain Objects Describing High-Throughput SNP Assays. |
| standardNormalization | Default complete normalization |
| [-method | Class to Contain Objects Describing High-Throughput SNP Assays. |