Normalization and reporting of Illumina SNP bead arrays


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Documentation for package `beadarraySNP' version 1.0.0

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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
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
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.
featureData,SnpSetIllumina-method Class to Contain Objects Describing High-Throughput SNP Assays.
featureData<-,SnpSetIllumina-method Class to Contain Objects Describing High-Throughput SNP Assays.
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.
normalizeBetweenAlleles.SNP between Allele normalization
normalizeLoci.SNP locus normalization
normalizeWithinArrays.SNP within Array normalization
pdfChromosomesSmoothCopyNumber reportWrappers
pdfQC QCreport
pdfSamplesSmoothCopyNumber reportWrappers
plotQC Spatial plots of array QC information
plotQC,QCIllumina-method Class "QCIllumina"
polar2RG Polar transformations
QC.260 Illumina example data
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
reportChromosomesSmoothCopyNumber Genomic reports
reporterInfo,SnpSetIllumina-method Class to Contain Objects Describing High-Throughput SNP Assays.
reporterInfo<-,SnpSetIllumina,data.frame-method Class to Contain Objects Describing High-Throughput SNP Assays.
reportSamplePanelQC reportSamplePanelQC
reportSamplePanelQC,QCIllumina-method reportSamplePanelQC
reportSamplePanelQC-methods reportSamplePanelQC
reportSamplesSmoothCopyNumber Genomic reports
RG2polar Polar transformations
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.