Normalization and reporting of Illumina SNP bead arrays


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Documentation for package ‘beadarraySNP’ version 1.6.0

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alterCN alterCN
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
BeadstudioQC Quality control of Beadstudio report files
calculateGSR Class to Contain Objects Describing High-Throughput SNP Assays.
calculateGSR,SnpSetIllumina-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
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
convert2aCGH Conversion to Copynumber analysis objects
convert2SegList Conversion to Copynumber analysis objects
createCNSummary Summarization of Copy number states
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.
fData,SnpSetIllumina-method Class to Contain Objects Describing High-Throughput SNP Assays.
fData<-,SnpSetIllumina,data.frame-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.
getDNAindex Calculate the DNA index based on assigned copy number values to probes
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.
interactiveCNselect Interactive assignment of copynumbers to genomic segments
normalizeBetweenAlleles.SNP between Allele normalization
normalizeLoci.SNP locus normalization
normalizeWithinArrays.SNP Within Array normalization
pdfBeadstudioQC Quality control of Beadstudio report files
pdfChromosomeGainLossLOH reportWrappers
pdfChromosomesSmoothCopyNumber reportWrappers
pdfQC QCreport
pdfSamplesSmoothCopyNumber reportWrappers
plotGoldenGate4OPA Plot Golden Gate genomic view
plotQC Spatial plots of array QC information
plotQC,QCIllumina-method Class "QCIllumina"
polar2RG Polar transformations
QC.260 Illumina example data
QCIllumina Class "QCIllumina"
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
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,QCIllumina-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.
standardNormalization Default complete normalization
[,SnpSetIllumina-method Class to Contain Objects Describing High-Throughput SNP Assays.