| calls |
Accessors for SnpCallSet |
| calls,SnpCallSet-method |
Accessors for SnpCallSet |
| calls<-,SnpCallSet,matrix-method |
Accessors for SnpCallSet |
| callsConfidence |
Accessors for SnpCallSet |
| callsConfidence,SnpCallSet-method |
Accessors for SnpCallSet |
| callsConfidence<-,SnpCallSet,matrix-method |
Accessors for SnpCallSet |
| chromosome |
Accessor for chromosome information |
| chromosome,TilingFeatureSet-method |
Accessor for chromosome information |
| cleanPlatformName |
Parser to CEL files |
| cnConfidence |
Accessors for SnpCopyNumberSet objects |
| cnConfidence,SnpCopyNumberSet-method |
Accessors for SnpCopyNumberSet objects |
| cnConfidence<-,SnpCopyNumberSet,matrix-method |
Accessors for SnpCopyNumberSet objects |
| copyNumber |
Accessors for SnpCopyNumberSet objects |
| copyNumber,SnpCopyNumberSet-method |
Accessors for SnpCopyNumberSet objects |
| copyNumber<-,SnpCopyNumberSet,matrix-method |
Accessors for SnpCopyNumberSet objects |
| crlmm |
Genotype Calls |
| geneNames,AffySNPPDInfo-method |
Internals |
| geneNames,FeatureSet-method |
Internals |
| geneNames,platformDesign-method |
Internals |
| genomeBuild |
Genome Build Information |
| genomeBuild,PDInfo-method |
Genome Build Information |
| genomeBuild,TilingFeatureSet-method |
Genome Build Information |
| geometry |
List fields in the (pm/mm)feature table |
| geometry,PDInfo-method |
List fields in the (pm/mm)feature table |
| getA |
Compute average log-intensities / log-ratios |
| getA,SnpCnvQSet-method |
Compute average log-intensities / log-ratios |
| getA,SnpQSet-method |
Compute average log-intensities / log-ratios |
| getChrXIndex |
Internals |
| getGenotypeRegionParams |
Internals |
| getM |
Compute average log-intensities / log-ratios |
| getM,SnpCnvQSet-method |
Compute average log-intensities / log-ratios |
| getM,SnpQSet-method |
Compute average log-intensities / log-ratios |
| getPD |
Retrieve Platform Design object |
| getPlatformDesign |
Retrieve Platform Design object |
| getPlatformDesign,FeatureSet-method |
Retrieve Platform Design object |
| getSnpFragmentLength |
Internals |
| manufacturer |
Accessor to the manufacturer slot. |
| manufacturer,FeatureSet-method |
Accessor to the manufacturer slot. |
| manufacturer,PDInfo-method |
Accessor to the manufacturer slot. |
| manufacturer<-,FeatureSet-method |
Accessor to the manufacturer slot. |
| MAplot |
MA plots |
| MAplot,FeatureSet-method |
MA plots |
| MAplot-methods |
MA plots |
| mm |
Accessor to the PM/MM matrices |
| mm,FeatureSet-method |
Accessor to the PM/MM matrices |
| mm<-,FeatureSet,BufferedMatrix-method |
Accessor to the PM/MM matrices |
| mm<-,FeatureSet,matrix-method |
Accessor to the PM/MM matrices |
| mmindex |
Extract PM or MM indexes |
| mmindex,AffySNPPDInfo-method |
Extract PM or MM indexes |
| mmindex,FeatureSet-method |
Extract PM or MM indexes |
| mmindex,platformDesign-method |
Extract PM or MM indexes |
| mmSequence |
Probe Sequeces |
| mmSequence,AffySNPPDInfo-method |
Probe Sequeces |
| mmSequence,FeatureSet-method |
Probe Sequeces |
| mmSequence,platformDesign-method |
Probe Sequeces |
| PDInfo-class |
Classes "PDInfo" and "SNPPDInfo" |
| platform |
Retrieve/replace platform information |
| platform,FeatureSet-method |
Retrieve/replace platform information |
| platform<-,FeatureSet-method |
Retrieve/replace platform information |
| platformDesign-class |
Class "platformDesign" |
| platformDesignName |
Internals |
| platformDesignName,FeatureSet-method |
Internals |
| plotDensity |
Plot density of intensities. |
| pm |
Accessor to the PM/MM matrices |
| pm,FeatureSet-method |
Accessor to the PM/MM matrices |
| pm,SnpCnvFeatureSet-method |
Accessor to the PM/MM matrices |
| pm<-,FeatureSet,BufferedMatrix-method |
Accessor to the PM/MM matrices |
| pm<-,FeatureSet,matrix-method |
Accessor to the PM/MM matrices |
| pmAllele |
Access the allele information for PM probes. |
| pmAllele,AffySNPPDInfo-method |
Access the allele information for PM probes. |
| pmAllele,PDInfo-method |
Access the allele information for PM probes. |
| pmAllele,SnpFeatureSet-method |
Access the allele information for PM probes. |
| pmChr |
Accessor for chromosome information |
| pmChr,TilingFeatureSet-method |
Accessor for chromosome information |
| pmindex |
Extract PM or MM indexes |
| pmindex,AffySNPCNVPDInfo-method |
Extract PM or MM indexes |
| pmindex,AffySNPPDInfo-method |
Extract PM or MM indexes |
| pmindex,FeatureSet-method |
Extract PM or MM indexes |
| pmindex,platformDesign-method |
Extract PM or MM indexes |
| pmindex,SnpCnvFeatureSet-method |
Extract PM or MM indexes |
| pmPosition |
Accessor to position information |
| pmPosition,AffySNPPDInfo-method |
Accessor to position information |
| pmPosition,TilingFeatureSet-method |
Accessor to position information |
| pmSequence |
Probe Sequeces |
| pmSequence,AffySNPPDInfo-method |
Probe Sequeces |
| pmSequence,FeatureSet-method |
Probe Sequeces |
| pmSequence,platformDesign-method |
Probe Sequeces |
| pmStrand |
Accessor to the strand information |
| pmStrand,AffySNPPDInfo-method |
Accessor to the strand information |
| position |
Accessor to position information |
| position,TilingFeatureSet-method |
Accessor to position information |
| probeNames |
Accessor to feature names |
| probeNames,AffySNPPDInfo-method |
Accessor to feature names |
| probeNames,FeatureSet-method |
Accessor to feature names |
| probeNames,platformDesign-method |
Accessor to feature names |