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A B C D E F G H I K L M N O P R S T misc
| oligo-package | The oligo package: a tool for analysis of oligonucleotide arrays |
| $,platformDesign-method | Internals |
| AffySNPPDInfo-class | Class "DBPDInfo" |
| antisenseThetaA | Summarized Measures for SNP |
| antisenseThetaA,SnpQSet-method | Summarized Measures for SNP |
| antisenseThetaB | Summarized Measures for SNP |
| antisenseThetaB,SnpQSet-method | Summarized Measures for SNP |
| basecontent | Sequence Base Contents |
| boxplot | Boxplot |
| boxplot,FeatureSet-method | Boxplot |
| 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 |
| db | Internals |
| db,DBPDInfo-method | Internals |
| DBPDInfo-class | Class "DBPDInfo" |
| ExonFeatureSet-class | "FeatureSet" Extensions |
| ExpressionFeatureSet-class | "FeatureSet" Extensions |
| exprs,FeatureSet-method | Internals |
| featureIndex | Indexes for features in the expression matrix |
| featureIndex,FeatureSet-method | Indexes for features in the expression matrix |
| featureInfo | Internals |
| featureInfo,platformDesign-method | Internals |
| FeatureSet-class | Classes for Feature level data |
| 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,SnpQSet-method | Compute average log-intensities / log-ratios |
| getChrXIndex | Internals |
| getGenotypeRegionParams | Internals |
| getM | 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 |
| hist | Density estimate |
| hist,FeatureSet-method | Density estimate |
| image | Display a Color Image |
| image,FeatureSet-method | Display a Color Image |
| initialize,DBPDInfo-method | Internals |
| initialize,FeatureSet-method | Internals |
| initialize,SnpCallSet-method | Internals |
| initialize,SnpCopyNumberSet-method | Internals |
| initialize,SnpQSet-method | Internals |
| kind | Array type |
| kind,AffySNPPDInfo-method | Array type |
| kind,platformDesign-method | Array type |
| length,FeatureSet-method | Internals |
| list.celfiles | List CEL/XYS files |
| list.xysfiles | List CEL/XYS files |
| listFeatureFields | List fields in the (pm/mm)feature table |
| listFeatureFields,AffySNPPDInfo-method | List fields in the (pm/mm)feature table |
| listFeatureFields,PDInfo-method | List fields in the (pm/mm)feature table |
| listFeatureSetFields | List fields in the (pm/mm)feature table |
| listFeatureSetFields,AffySNPPDInfo-method | List fields in the (pm/mm)feature table |
| listFeatureSetFields,PDInfo-method | List fields in the (pm/mm)feature table |
| 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. |
| 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 |
| names,platformDesign-method | Internals |
| ncol | ~~function to do ... ~~ |
| ncol,platformDesign-method | ~~function to do ... ~~ |
| normalizeToSample | Internals |
| nProbes | Count number of probes |
| nProbes,AffySNPPDInfo-method | Count number of probes |
| nProbes,platformDesign-method | Count number of probes |
| nrow | ~~function to do ... ~~ |
| nrow,platformDesign-method | ~~function to do ... ~~ |
| oligoSnpSet-class | "SnpSet" Extensions |
| 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<-,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,AffySNPPDInfo-method | Extract PM or MM indexes |
| pmindex,FeatureSet-method | Extract PM or MM indexes |
| pmindex,platformDesign-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 |
| read.celfiles | Parser to CEL files |
| read.xysfiles | Parser to XYS files |
| rma | RMA |
| rma,FeatureSet-method | RMA |
| senseThetaA | Summarized Measures for SNP |
| senseThetaA,SnpQSet-method | Summarized Measures for SNP |
| senseThetaB | Summarized Measures for SNP |
| senseThetaB,SnpQSet-method | Summarized Measures for SNP |
| sequenceDesignMatrix | Create design matrix for sequences |
| show,PDInfo-method | Internals |
| show,platformDesign-method | Internals |
| SnpCallSet-class | "SnpSet" Extensions |
| SnpCopyNumberSet-class | "SnpSet" Extensions |
| SnpFeatureSet-class | "FeatureSet" Extensions |
| SNPPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| SnpQSet-class | Class "SnpQSet" |
| snprma | Preprocessing SNP Arrays |
| TilingFeatureSet-class | "FeatureSet" Extensions |
| [,FeatureSet-method | Internals |