Entry: HmmPredict-class
Aliases: HmmPredict-class
Keywords: classes
Description: Class for containing output from a hidden Markov fit to SNP-level data of genotype calls and copy number estimates
URL: ../../../library/SNPchip/html/HmmPredict-class.html

Entry: ParESet-class
Aliases: ParESet-class $,ParESet-method $<-,ParESet-method hmmPredict,ParESet-method initialize,ParESet-method plotSnp,ParESet,SnpLevelSet-method snpPar,ParESet-method snpPar<-,ParESet-method snpset,ParESet-method
Keywords: classes
Description: Class "ParESet"
URL: ../../../library/SNPchip/html/ParESet-class.html

Entry: ParSnpCallSet-class
Aliases: ParSnpCallSet-class initialize,ParSnpCallSet-method
Keywords: classes
Description: Class "ParSnpCallSet"
URL: ../../../library/SNPchip/html/ParSnpCallSet-class.html

Entry: ParSnpCopyNumberSet-class
Aliases: ParSnpCopyNumberSet-class initialize,ParSnpCopyNumberSet-method
Keywords: classes
Description: Class "ParSnpCopyNumberSet"
URL: ../../../library/SNPchip/html/ParSnpCopyNumberSet-class.html

Entry: ParSnpSet-class
Aliases: ParSnpSet-class initialize,ParSnpSet-method
Keywords: classes
Description: Class "ParSnpSet"
URL: ../../../library/SNPchip/html/ParSnpSet-class.html

Entry: RatioSnpSet-class
Aliases: RatioSnpSet-class
Keywords: classes
Description: Class for high throughput SNP-level data. The assay data contains ratios of copy number.
URL: ../../../library/SNPchip/html/RatioSnpSet-class.html

Entry: RatioSnpSet-methods
Aliases: RatioSnpSet-methods initialize,RatioSnpSet-method ratio ratio<- ratio,RatioSnpSet-method ratio,SnpLevelSet-method ratio<-,SnpLevelSet,matrix-method cnConfidence,RatioSnpSet-method cnConfidence<-,RatioSnpSet,matrix-method copyNumber,RatioSnpSet-method copyNumber<-,RatioSnpSet,matrix-method ratioConfidence ratioConfidence<- ratioConfidence,RatioSnpSet-method ratioConfidence<-,RatioSnpSet,matrix-method
Keywords: manip
Description: Accessors for RatioSnpSet objects
URL: ../../../library/SNPchip/html/RatioSnpSet-methods.html

Entry: addFeatureData-methods
Aliases: addFeatureData addFeatureData-methods addFeatureData,eSet-method
Keywords: methods
Description: Method for Function addFeatureData
URL: ../../../library/SNPchip/html/addFeatureData-method.html

Entry: alleleA
Aliases: alleleA alleleA,AnnotatedDataFrame-method alleleA,SnpLevelSet-method
Keywords: methods
Description: Accessor for the A allele
URL: ../../../library/SNPchip/html/alleleA.html

Entry: alleleB
Aliases: alleleB alleleB,SnpLevelSet-method alleleB,AnnotatedDataFrame-method
Keywords: methods
Description: Accessor for the B allele
URL: ../../../library/SNPchip/html/alleleB.html

Entry: centromere
Aliases: centromere
Keywords: manip
Description: Coordinates of centromere
URL: ../../../library/SNPchip/html/centromere.html

Entry: chromosome2integer
Aliases: chromosome2integer integer2chromosome
Keywords: manip
Description: Converts chromosome to integer or vice versa
URL: ../../../library/SNPchip/html/chromosome2integer.html

Entry: chromosomeAnnotation
Aliases: chromosomeAnnotation
Keywords: datasets
Description: chromosome annotation
URL: ../../../library/SNPchip/html/chromosomeAnnotation.html

Entry: chromosomeSize
Aliases: chromosomeSize
Keywords: manip
Description: Size of chromosome in number of base pairs.
URL: ../../../library/SNPchip/html/chromosomeSize.html

Entry: coerce-methods
Aliases: coerce-methods coerce,oligoSnpSet,SnpCallSet-method coerce,oligoSnpSet,SnpCopyNumberSet-method coerce,AnnotatedSnpSet,oligoSnpSet-method coerce,AnnotatedSnpCallSet,SnpCallSet-method coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method
Keywords: methods
Description: Methods for Function coerce
URL: ../../../library/SNPchip/html/coerce-methods.html

Entry: crlmmOut
Aliases: crlmmOut
Keywords: datasets
Description: A data object created by the oligo vignette
URL: ../../../library/SNPchip/html/crlmmOut.html

Entry: cytoband
Aliases: cytoband
Keywords: datasets
Description: Start and stop sites of cytoband
URL: ../../../library/SNPchip/html/cytoband.html

Entry: dbSnpId
Aliases: dbSnpId dbSnpId,AnnotatedDataFrame-method dbSnpId,SnpLevelSet-method
Keywords: manip
Description: The dbSNP identifier
URL: ../../../library/SNPchip/html/dbSnpId.html

Entry: enzyme
Aliases: enzyme enzyme,SnpLevelSet-method enzyme,AnnotatedDataFrame-method
Keywords: methods
Description: Enzyme used to digest DNA
URL: ../../../library/SNPchip/html/enzyme.html

Entry: featureData-accessors
Aliases: chromosome chromosome-methods chromosome,SnpLevelSet-method chromosome,SnpCallSet-method chromosome,SnpCopyNumberSet-method chromosome,oligoSnpSet-method chromosome,AnnotatedDataFrame-method position position-methods position,SnpLevelSet-method position,SnpCallSet-method position,SnpCopyNumberSet-method position,oligoSnpSet-method position,AnnotatedDataFrame-method position,SnpLevelSet-method
Keywords: methods manip
Description: Accessors for feature-level SNP annotation
URL: ../../../library/SNPchip/html/featureData-accessors.html

Entry: fragmentLength
Aliases: fragmentLength fragmentLength,AnnotatedDataFrame-method fragmentLength,SnpLevelSet-method
Keywords: manip
Description: Accessor for the fragment length
URL: ../../../library/SNPchip/html/fragmentLength.html

Entry: getPar
Aliases: getPar getPar,ParESet-method
Keywords: manip methods
Description: Adds graphical parameters for plotting SNP data
URL: ../../../library/SNPchip/html/getPar.html

Entry: hapmap
Aliases: hapmap
Keywords: datasets
Description: Data from the hapmap project
URL: ../../../library/SNPchip/html/hapmap.html

Entry: hmmPredict
Aliases: hmmPredict
Keywords: methods
Description: Accessor for HMM output
URL: ../../../library/SNPchip/html/hmmPredict.html

Entry: plotCytoband
Aliases: plotCytoband
Keywords: aplot
Description: Plots cytoband for one chromosome
URL: ../../../library/SNPchip/html/plotCytoband.html

Entry: plotPredictions
Aliases: plotPredictions
Keywords: aplot
Description: Plots the predictions from the HMM
URL: ../../../library/SNPchip/html/plotPredictions.html

Entry: plotSnp
Aliases: plotSnp plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method plotSnp,ParSnpCallSet,SnpCallSet-method plotSnp,ParSnpSet,oligoSnpSet-method plotSnp,SnpLevelSet-method plot,ParSnpCopyNumberSet,SnpCopyNumberSet-method plot,ParSnpCallSet,SnpCallSet-method plot,ParSnpSet,oligoSnpSet-method plot,SnpLevelSet-method
Keywords: hplot
Description: Plots copy number and genotype calls against physical position
URL: ../../../library/SNPchip/html/plotSnp.html

Entry: sample.snpset
Aliases: sample.snpset
Keywords: datasets
Description: Example object of class oligoSnpSet
URL: ../../../library/SNPchip/html/sample.snpset.html

Entry: selectSomeIndex
Aliases: selectSomeIndex selectSomeIndex,data.frame-method
Keywords: methods
Description: Method from Biobase for selecting indices
URL: ../../../library/SNPchip/html/selectSomeIndex.html

Entry: show-methods
Aliases: show-methods show,oligoSnpSet-method show,ParESet-method show,ParSnpCopyNumberSet-method show,ParSnpCallSet-method show,ParSnpSet-method
Keywords: methods
Description: show methods
URL: ../../../library/SNPchip/html/show-methods.html

Entry: showSummary
Aliases: showSummary
Keywords: aplot
Description: Displays descriptive statistics for a sample.
URL: ../../../library/SNPchip/html/showSummary.html

Entry: smoothSnp
Aliases: smoothSnp smoothSnp,oligoSnpSet-method
Keywords: methods
Description: A simple nonparametric smoother for genotype and copy number
URL: ../../../library/SNPchip/html/smoothSnp.html

Entry: snpPar
Aliases: snpPar snpPar<-
Keywords: methods
Description: Accessor for graphical parameters
URL: ../../../library/SNPchip/html/snpPar.html

Entry: snpset
Aliases: snpset
Keywords: methods
Description: Accessor for SNP data
URL: ../../../library/SNPchip/html/snpset.html

Entry: summary-methods
Aliases: summary-methods summary,ANY-method summary,SnpCallSet-method summary,AnnotatedSnpSet-method summary,oligoSnpSet-method
Keywords: methods
Description: Methods for Function summary
URL: ../../../library/SNPchip/html/summary-methods.html

Entry: updateObject-methods
Aliases: updateObject,oligoSnpSet-method
Keywords: methods
Description: updateObject methods
URL: ../../../library/SNPchip/html/updateObject-methods.html
