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. |