# Normalization and reporting of Illumina SNP bead arrays

## Documentation for package ‘beadarraySNP’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.