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. |