Entry: copynumberConversion
Aliases: convert2aCGH convert2SegList
Keywords: manip
Description: Conversion to Copynumber analysis objects
URL: ../../../library/beadarraySNP/html/CopynumberConversion.html

Entry: Illumina Genomic data
Aliases: chr17.260 QC.260
Keywords: datasets
Description: Illumina example data
URL: ../../../library/beadarraySNP/html/Datasets.html

Entry: GenomicReports
Aliases: reportChromosomesSmoothCopyNumber reportSamplesSmoothCopyNumber reportGenomeGainLossLOH reportChromosomeGainLossLOH reportGenomeIntensityPlot
Keywords: manip
Description: Genomic reports
URL: ../../../library/beadarraySNP/html/GenomicReports.html

Entry: PolarTransforms
Aliases: RG2polar polar2RG
Keywords: manip
Description: Polar transformations
URL: ../../../library/beadarraySNP/html/PolarTransforms.html

Entry: QCIllumina-class
Aliases: QCIllumina-class arrayID,QCIllumina-method arrayID<-,QCIllumina-method arrayType,QCIllumina-method arrayType<-,QCIllumina-method initialize,QCIllumina-method plotQC,QCIllumina-method
Keywords: classes
Description: Class "QCIllumina"
URL: ../../../library/beadarraySNP/html/QCIllumina-class.html

Entry: alterCN
Aliases: alterCN
Keywords: manip
Description: alterCN
URL: ../../../library/beadarraySNP/html/alterCN.html

Entry: QCaccessors
Aliases: arrayType arrayType<- arrayID arrayID<-
Keywords: manip
Description: Accessor methods for QC objects
URL: ../../../library/beadarraySNP/html/arrayType.html

Entry: backgroundCorrect.SNP
Aliases: backgroundCorrect.SNP
Keywords: manip
Description: Background correction
URL: ../../../library/beadarraySNP/html/backgroundCorrect.SNP.html

Entry: backgroundEstimate
Aliases: backgroundEstimate
Keywords: manip
Description: Estimate background intensities from foreground intensity
URL: ../../../library/beadarraySNP/html/backgroundEstimate.html

Entry: calculateLOH
Aliases: calculateLOH
Keywords: manip
Description: Determine LOH in experiment
URL: ../../../library/beadarraySNP/html/calculateLOH.html

Entry: calculateQCarray
Aliases: calculateQCarray
Keywords: manip
Description: Retrieve QC information from a SnpSetIllumina object
URL: ../../../library/beadarraySNP/html/calculateQCarray.html

Entry: SnpSetIllumina
Aliases: class:SnpSetIllumina SnpSetIllumina SnpSetIllumina-class exprs<-,SnpSetIllumina,matrix-method reporterInfo,SnpSetIllumina-method reporterInfo<-,SnpSetIllumina,data.frame-method exprs,SnpSetIllumina-method [,SnpSetIllumina-method initialize,SnpSetIllumina-method combine,SnpSetIllumina,SnpSetIllumina-method combine,SnpSetIllumina,ANY-method featureData<-,SnpSetIllumina-method featureData,SnpSetIllumina-method calculateGSR,SnpSetIllumina-method calculateGSR
Keywords: classes
Description: Class to Contain Objects Describing High-Throughput SNP Assays.
URL: ../../../library/beadarraySNP/html/class.SnpSetIllumina.html

Entry: compareGenotypes
Aliases: compareGenotypes
Keywords: manip
Description: Compare genotypes
URL: ../../../library/beadarraySNP/html/compareGenotypes.html

Entry: createCNSummary
Aliases: createCNSummary
Keywords: manip
Description: Summarization of Copy number states
URL: ../../../library/beadarraySNP/html/createCNSummary.html

Entry: getDNAindex
Aliases: getDNAindex
Keywords: manip
Description: Calculate the DNA index based on assigned copy number values to probes
URL: ../../../library/beadarraySNP/html/getDNAindex.html

Entry: heterozygosity
Aliases: heterozygosity
Keywords: manip
Description: Find regions of homozygous SNPs
URL: ../../../library/beadarraySNP/html/heterozygosity.html

Entry: heterozygousSNPs
Aliases: heterozygousSNPs
Keywords: manip
Description: Retrieve heterozygous SNPs
URL: ../../../library/beadarraySNP/html/heterozygousSNPs.html

Entry: interactiveCNselect
Aliases: interactiveCNselect
Keywords: manip iplot
Description: Interactive assignment of copynumbers to genomic segments
URL: ../../../library/beadarraySNP/html/interactiveCNselect.html

Entry: normalizeBetweenAlleles.SNP
Aliases: normalizeBetweenAlleles.SNP
Keywords: manip
Description: between Allele normalization
URL: ../../../library/beadarraySNP/html/normalizeBetweenAlleles.SNP.html

Entry: normalizeLoci.SNP
Aliases: normalizeLoci.SNP
Keywords: manip
Description: locus normalization
URL: ../../../library/beadarraySNP/html/normalizeLoci.SNP.html

Entry: normalizeWithinArrays.SNP
Aliases: normalizeWithinArrays.SNP
Keywords: manip
Description: within Array normalization
URL: ../../../library/beadarraySNP/html/normalizeWithinArrays.SNP.html

Entry: pdfChromosomesSmoothCopyNumber
Aliases: pdfChromosomesSmoothCopyNumber pdfSamplesSmoothCopyNumber pdfChromosomeGainLossLOH
Keywords: hplot
Description: reportWrappers
URL: ../../../library/beadarraySNP/html/pdfChromosomesSmoothCopyNumber.html

Entry: pdfQC
Aliases: pdfQC
Keywords: hplot
Description: QCreport
URL: ../../../library/beadarraySNP/html/pdfQC.html

Entry: plotGoldenGate4OPA
Aliases: plotGoldenGate4OPA
Keywords: hplot iplot
Description: Plot Golden Gate genomic view
URL: ../../../library/beadarraySNP/html/plotGoldenGate4OPA.html

Entry: plotQC
Aliases: plotQC
Keywords: hplot
Description: Spatial plots of array QC information
URL: ../../../library/beadarraySNP/html/plotQC.html

Entry: read.SnpSetIllumina
Aliases: read.SnpSetIllumina
Keywords: file manip
Description: Read Experimental Data and into an 'SnpSetIllumina' Object
URL: ../../../library/beadarraySNP/html/read.SnpSetIllumina.html

Entry: removeLowQualityProbes
Aliases: removeLowQualityProbes
Keywords: manip
Description: Quality control of SnpSetIllumina objects
URL: ../../../library/beadarraySNP/html/removeLowQualityProbes.html

Entry: removeLowQualitySamples
Aliases: removeLowQualitySamples
Keywords: manip
Description: Quality control of SnpSetIllumina objects
URL: ../../../library/beadarraySNP/html/removeLowQualitySamples.html

Entry: renameOPA
Aliases: renameOPA
Keywords: manip
Description: Change the linkage panel in a dataset
URL: ../../../library/beadarraySNP/html/renameOPA.html

Entry: reportGenotypeSegmentation
Aliases: reportGenotypeSegmentation
Keywords: hplot
Description: plot genomic view
URL: ../../../library/beadarraySNP/html/reportGenotypeSegmentation.html

Entry: reportSamplePanelQC-methods
Aliases: reportSamplePanelQC-methods reportSamplePanelQC reportSamplePanelQC,QCIllumina-method
Keywords: methods hplot
Description: reportSamplePanelQC
URL: ../../../library/beadarraySNP/html/reportSamplePanelQC-methods.html

Entry: segmentate
Aliases: segmentate
Keywords: manip
Description: Segmentation for SnpSetIllumina objects
URL: ../../../library/beadarraySNP/html/segmentate.html

Entry: setRealCN
Aliases: setRealCN
Keywords: manip
Description: Integrate state information into SNP object
URL: ../../../library/beadarraySNP/html/setRealCN.html

Entry: smoothed.intensity
Aliases: smoothed.intensity
Keywords: manip
Description: Smooth intensity data
URL: ../../../library/beadarraySNP/html/smoothed.intensity.html

Entry: standardNormalization
Aliases: standardNormalization
Keywords: manip
Description: Default complete normalization
URL: ../../../library/beadarraySNP/html/standardNormalization.html
