Entry: DBPDInfo-class
Aliases: DBPDInfo-class AffySNPPDInfo-class
Keywords: classes
Description: Class "DBPDInfo"
URL: ../../../library/oligo/html/DBPDInfo-class.html

Entry: FeatureSet-class
Aliases: FeatureSet-class
Keywords: classes
Description: Classes for Feature level data
URL: ../../../library/oligo/html/FeatureSet-class.html

Entry: ExonFeatureSet-class
Aliases: ExpressionFeatureSet-class ExonFeatureSet-class SnpFeatureSet-class TilingFeatureSet-class
Keywords: classes
Description: "FeatureSet" Extensions
URL: ../../../library/oligo/html/FeatureSetExtensions-class.html

Entry: mmindex
Aliases: mmindex pmindex mmindex,AffySNPPDInfo-method pmindex,AffySNPPDInfo-method pmindex,AffySNPCNVPDInfo-method mmindex,FeatureSet-method pmindex,FeatureSet-method pmindex,SnpCnvFeatureSet-method mmindex,platformDesign-method pmindex,platformDesign-method pmindex,ExpressionPDInfo-method pmindex,TilingPDInfo-method mmindex,ExpressionPDInfo-method mmindex,TilingPDInfo-method
Keywords: manip
Description: Extract PM or MM indexes
URL: ../../../library/oligo/html/Index-methods.html

Entry: mm
Aliases: mm pm mm,FeatureSet-method pm,FeatureSet-method pm,SnpCnvFeatureSet-method mm<- pm<- mm<-,FeatureSet,matrix-method pm<-,FeatureSet,matrix-method mm<-,FeatureSet,BufferedMatrix-method pm<-,FeatureSet,BufferedMatrix-method
Keywords: manip
Description: Accessor to the PM/MM matrices
URL: ../../../library/oligo/html/IntensityMatrix-methods.html

Entry: MAplot-methods
Aliases: MAplot MAplot-methods MAplot,FeatureSet-method
Keywords: methods
Description: MA plots
URL: ../../../library/oligo/html/MAplot-methods.html

Entry: PDInfo-class
Aliases: PDInfo-class SNPPDInfo-class
Keywords: classes
Description: Classes "PDInfo" and "SNPPDInfo"
URL: ../../../library/oligo/html/PDInfo-class.html

Entry: listFeatureFields
Aliases: listFeatureFields listFeatureSetFields listFeatureFields,PDInfo-method listFeatureSetFields,PDInfo-method listFeatureFields,AffySNPPDInfo-method listFeatureSetFields,AffySNPPDInfo-method geometry geometry,PDInfo-method
Keywords: manip
Description: List fields in the (pm/mm)feature table
URL: ../../../library/oligo/html/PDInfo-methods.html

Entry: mmSequence
Aliases: mmSequence pmSequence mmSequence,FeatureSet-method pmSequence,FeatureSet-method mmSequence,platformDesign-method pmSequence,platformDesign-method mmSequence,AffySNPPDInfo-method pmSequence,AffySNPPDInfo-method pmSequence,AffySNPCNVPDInfo-method pmSequence,ExpressionPDInfo-method pmSequence,TilingPDInfo-method
Keywords: manip
Description: Probe Sequeces
URL: ../../../library/oligo/html/Sequences-methods.html

Entry: SnpQSet-class
Aliases: SnpQSet-class
Keywords: classes
Description: Class "SnpQSet"
URL: ../../../library/oligo/html/SnpQSet-class.html

Entry: getA
Aliases: getA getM getA,SnpQSet-method getM,SnpQSet-method getA,SnpCnvQSet-method getM,SnpCnvQSet-method getM,TilingQSet-method
Keywords: manip
Description: Compute average log-intensities / log-ratios
URL: ../../../library/oligo/html/SnpQSet-methods.html

Entry: SnpCallSet-class
Aliases: SnpCallSet-class SnpCopyNumberSet-class oligoSnpSet-class
Keywords: classes
Description: "SnpSet" Extensions
URL: ../../../library/oligo/html/SnpSetExtensions-class.html

Entry: basecontent
Aliases: basecontent
Keywords: manip
Description: Sequence Base Contents
URL: ../../../library/oligo/html/basecontent.html

Entry: boxplot
Aliases: boxplot boxplot,FeatureSet-method boxplot,ExpressionSet-method
Keywords: hplot
Description: Boxplot
URL: ../../../library/oligo/html/boxplot.html

Entry: chromosome
Aliases: pmChr pmChr,TilingFeatureSet-method
Keywords: manip
Description: Accessor for chromosome information
URL: ../../../library/oligo/html/chromosome.html

Entry: crlmm
Aliases: crlmm justCRLMM
Keywords: classif
Description: Genotype Calls
URL: ../../../library/oligo/html/crlmm.html

Entry: featureIndex
Aliases: featureIndex featureIndex,FeatureSet-method
Keywords: manip
Description: Indexes for features in the expression matrix
URL: ../../../library/oligo/html/featureIndex.html

Entry: featureNames-methods
Aliases: featureNames-methods featureNames,FeatureSet-method
Keywords: methods
Description: Retrieve featureNames
URL: ../../../library/oligo/html/featureNames-methods.html

Entry: genomeBuild
Aliases: genomeBuild genomeBuild,TilingFeatureSet-method genomeBuild,PDInfo-method genomeBuild,FeatureSet-method
Keywords: manip
Description: Genome Build Information
URL: ../../../library/oligo/html/genomeBuild.html

Entry: getCrlmmSummaries
Aliases: getCrlmmSummaries
Keywords: manip
Description: Function to get CRLMM summaries saved to disk
URL: ../../../library/oligo/html/getCrlmmSummaries.html

Entry: getPlatformDesign
Aliases: getPlatformDesign getPD getPlatformDesign,FeatureSet-method
Keywords: manip
Description: Retrieve Platform Design object
URL: ../../../library/oligo/html/getPlatformDesign.html

Entry: hist
Aliases: hist hist,FeatureSet-method hist,ExpressionSet-method
Keywords: hplot
Description: Density estimate
URL: ../../../library/oligo/html/hist.html

Entry: image
Aliases: image image,FeatureSet-method
Keywords: hplot
Description: Display a Color Image
URL: ../../../library/oligo/html/image.html

Entry: getChrXIndex
Aliases: getChrXIndex getGenotypeRegionParams getSnpFragmentLength normalizeToSample initialize,DBPDInfo-method initialize,FeatureSet-method initialize,SnpCallSet-method initialize,SnpCopyNumberSet-method initialize,SnpQSet-method show,PDInfo-method show,platformDesign-method length,FeatureSet-method featureInfo featureInfo,platformDesign-method show,FeatureSet-method show,PDInfo-method show,platformDesign-method names,platformDesign-method platformDesignName platformDesignName,FeatureSet-method geneNames,AffySNPPDInfo-method geneNames,ExpressionPDInfo-method geneNames,TilingPDInfo-method geneNames,platformDesign-method geneNames,FeatureSet-method $,platformDesign-method [,FeatureSet-method db db,DBPDInfo-method db,SnpCallSet-method db,SnpCopyNumberSet-method db,SnpQSet-method db,SnpCnvQSet-method db,SnpFeatureSet-method db,FeatureSet-method exprs,FeatureSet-method
Keywords: manip
Description: Internals
URL: ../../../library/oligo/html/internals.html

Entry: justSNPRMA
Aliases: justSNPRMA
Keywords: manip
Description: Summarization of SNP data
URL: ../../../library/oligo/html/justSNPRMA.html

Entry: kind
Aliases: kind kind,platformDesign-method kind,AffySNPPDInfo-method kind,AffySNPCNVPDInfo-method kind,ExpressionPDInfo-method kind,TilingPDInfo-method kind,AffyExpressionPDInfo-method kind,AffyGenePDInfo-method
Keywords: manip
Description: Array type
URL: ../../../library/oligo/html/kind.html

Entry: list.celfiles
Aliases: list.celfiles list.xysfiles
Keywords: file
Description: List CEL/XYS files
URL: ../../../library/oligo/html/list.celfiles.html

Entry: manufacturer
Aliases: manufacturer manufacturer,FeatureSet-method manufacturer,PDInfo-method manufacturer<- manufacturer<-,FeatureSet-method
Keywords: manip
Description: Accessor to the manufacturer slot.
URL: ../../../library/oligo/html/manufacturer.html

Entry: nProbes
Aliases: nProbes nProbes,platformDesign-method nProbes,AffySNPPDInfo-method nProbes,ExpressionPDInfo-method nProbes,TilingPDInfo-method
Keywords: manip
Description: Count number of probes
URL: ../../../library/oligo/html/nProbes.html

Entry: ncol
Aliases: ncol ncol,platformDesign-method nrow nrow,platformDesign-method
Keywords: manip
Description: ~~function to do ... ~~
URL: ../../../library/oligo/html/ncol.html

Entry: oligo-package
Aliases: oligo-package
Keywords: package
Description: The oligo package: a tool for analysis of oligonucleotide arrays
URL: ../../../library/oligo/html/oligo-package.html

Entry: platform
Aliases: platform platform<- platform,FeatureSet-method platform<-,FeatureSet-method
Keywords: manip
Description: Retrieve/replace platform information
URL: ../../../library/oligo/html/platform.html

Entry: platformDesign-class
Aliases: platformDesign-class
Keywords: classes
Description: Class "platformDesign"
URL: ../../../library/oligo/html/platformDesign-class.html

Entry: plotM-methods
Aliases: plotM plotM-methods plotM,SnpQSet,character-method plotM,SnpQSet,integer-method plotM,SnpQSet,numeric-method plotM,TilingQSet,missing-method
Keywords: methods
Description: Methods for Log-Ratio plotting
URL: ../../../library/oligo/html/plotM-methods.html

Entry: pmAllele
Aliases: pmAllele pmAllele,SnpFeatureSet-method pmAllele,PDInfo-method pmAllele,AffySNPPDInfo-method
Keywords: manip
Description: Access the allele information for PM probes.
URL: ../../../library/oligo/html/pmAllele.html

Entry: pmPosition
Aliases: pmPosition pmOffset pmOffset,AffySNPPDInfo-method pmPosition,TilingFeatureSet-method position,TilingFeatureSet-method position,SnpCallSet-method pmPosition,ExpressionPDInfo-method pmPosition,TilingPDInfo-method
Keywords: manip
Description: Accessor to position information
URL: ../../../library/oligo/html/pmPosition.html

Entry: pmStrand
Aliases: pmStrand pmStrand,AffySNPPDInfo-method
Keywords: manip
Description: Accessor to the strand information
URL: ../../../library/oligo/html/pmStrand.html

Entry: probeNames
Aliases: probeNames probeNames,FeatureSet-method probeNames,AffySNPPDInfo-method probeNames,platformDesign-method probeNames,ExpressionPDInfo-method probeNames,TilingPDInfo-method
Keywords: manip
Description: Accessor to feature names
URL: ../../../library/oligo/html/probeNames.html

Entry: read.celfiles
Aliases: read.celfiles cleanPlatformName
Keywords: IO
Description: Parser to CEL files
URL: ../../../library/oligo/html/read.celfiles.html

Entry: read.xysfiles
Aliases: read.xysfiles
Keywords: IO
Description: Parser to XYS files
URL: ../../../library/oligo/html/read.xysfiles.html

Entry: readSummaries
Aliases: readSummaries
Keywords: manip
Description: Read summaries generated by crlmm
URL: ../../../library/oligo/html/readSummaries.html

Entry: rma
Aliases: rma rma,FeatureSet-method
Keywords: manip
Description: RMA
URL: ../../../library/oligo/html/rma.html

Entry: sequenceDesignMatrix
Aliases: sequenceDesignMatrix
Keywords: manip
Description: Create design matrix for sequences
URL: ../../../library/oligo/html/sequenceDesignMatrix.html

Entry: snprma
Aliases: snprma
Keywords: manip
Description: Preprocessing SNP Arrays
URL: ../../../library/oligo/html/snprma.html

Entry: antisenseThetaA
Aliases: antisenseThetaA antisenseThetaB senseThetaA senseThetaB antisenseThetaA,SnpQSet-method antisenseThetaB,SnpQSet-method senseThetaA,SnpQSet-method senseThetaB,SnpQSet-method
Keywords: manip
Description: Summarized Measures for SNP
URL: ../../../library/oligo/html/snprmaSummaries.html
