alterCN |
alterCN |
arrayID |
Accessor methods for QC objects |
arrayID,QCIllumina-method |
Class "QCIllumina" |
arrayID<- |
Accessor methods for QC objects |
arrayID<-,QCIllumina-method |
Class "QCIllumina" |
arrayType |
Accessor methods for QC objects |
arrayType,QCIllumina-method |
Class "QCIllumina" |
arrayType<- |
Accessor methods for QC objects |
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 |
calculateSmooth |
Class to Contain Objects Describing High-Throughput SNP Assays. |
calculateSmooth,SnpSetIllumina,character-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,SnpSetSegments-method |
Class "SnpSetSegments" |
cn.segments<- |
Class "SnpSetSegments" |
cn.segments<-,SnpSetSegments,list-method |
Class "SnpSetSegments" |
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 |
dist.GT |
~~function to do ... ~~ |
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. |
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,QCIllumina-method |
Class "QCIllumina" |
initialize,SnpSetIllumina-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
initialize,SnpSetSegments-method |
Class "SnpSetSegments" |
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,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. |
SnpSetSegments-class |
Class "SnpSetSegments" |
sortGenomic |
Class to Contain Objects Describing High-Throughput SNP Assays. |
sortGenomic,SnpSetIllumina-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
standardNormalization |
Default complete normalization |
[,SnpSetIllumina-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |