Man pages for beadarraySNP
Normalization and reporting of Illumina SNP bead arrays
| alterCN | alterCN |
| arrayType | Accessor methods for QC objects |
| backgroundCorrect.SNP | Background correction |
| backgroundEstimate | Estimate background intensities from foreground intensity |
| BeadstudioQC | Quality control of Beadstudio report files |
| calculateLOH | Determine LOH in experiment |
| calculateQCarray | Retrieve QC information from a SnpSetIllumina object |
| class.SnpSetIllumina | Class to Contain Objects Describing High-Throughput SNP... |
| compareGenotypes | Compare genotypes |
| CopynumberConversion | Conversion to Copynumber analysis objects |
| createCNSummary | Summarization of Copy number states |
| Datasets | Illumina example data |
| dist.GT | dist.GT |
| GenomicReports | Genomic reports |
| GetBeadStudioSampleNames | Extract samplenames from a report file |
| getDNAindex | Calculate the DNA index based on assigned copy number values... |
| heterozygosity | Find regions of homozygous SNPs |
| heterozygousSNPs | Retrieve heterozygous SNPs |
| 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 |
| pdfChromosomesSmoothCopyNumber | reportWrappers |
| pdfQC | QCreport |
| plotGoldenGate4OPA | Plot Golden Gate genomic view |
| plotQC | Spatial plots of array QC information |
| PolarTransforms | Polar transformations |
| QCIllumina-class | Class "QCIllumina" |
| read.SnpSetIllumina | Read Experimental Data, Featuredata and Phenodata into an... |
| removeLowQualityProbes | Quality control of SnpSetIllumina objects |
| removeLowQualitySamples | Quality control of SnpSetIllumina objects |
| renameOPA | Change the linkage panel in a dataset |
| reportGenotypeSegmentation | plot genomic view |
| reportSamplePanelQC-methods | reportSamplePanelQC |
| 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 |
| SnpSetSegments-class | Class "SnpSetSegments" |
| standardNormalization | Default complete normalization |
