Entry: DEPRECATED-classes
Aliases: AnnotatedSnpSet-class AnnotatedSnpCallSet-class AnnotatedSnpCopyNumberSet-class
Keywords: classes
Description: Deprecated classes
URL: ../../../library/SNPchip/html/DEPRECATED-classes.html

Entry: ParESet-class
Aliases: ParESet-class $,ParESet-method $<-,ParESet-method allPlots,ParESet-method initialize,ParESet-method snpPar,ParESet-method snpPar<-,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: addFeatureData-methods
Aliases: addFeatureData addFeatureData-methods addFeatureData,eSet-method
Keywords: methods
Description: Method for Function addFeatureData
URL: ../../../library/SNPchip/html/addFeatureData-method.html

Entry: allPlots-methods
Aliases: allPlots
Keywords: methods
Description: Extracts graphical parameters to be used by all plotting devices
URL: ../../../library/SNPchip/html/allPlots-methods.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: calculateCopyNumber-methods
Aliases: calculateCopyNumber calculateCopyNumber-methods calculateCopyNumber,SnpQSet-method
Keywords: methods manip
Description: Extracts copy number estimates from thetas in SnpQSet object
URL: ../../../library/SNPchip/html/calculateCopyNumber.html

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

Entry: chromosome-methods
Aliases: chromosome chromosome-methods chromosome,SnpLevelSet-method chromosome,AnnotatedDataFrame-method
Keywords: methods manip
Description: Accessor for chromosome SNP annotation
URL: ../../../library/SNPchip/html/chromosome.html

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

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

Entry: coerce-methods
Aliases: coerce-methods 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: 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: 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-methods
Aliases: getPar getPar-methods getPar,SnpLevelSet-method
Keywords: methods
Description: Computes default graphical parameters
URL: ../../../library/SNPchip/html/getPar-methods.html

Entry: getSnpAnnotation
Aliases: getSnpAnnotation getSnpAnnotation,SnpLevelSet-method getSnpAnnotation,SnpCallSet-method getSnpAnnotation,SnpCopyNumberSet-method getSnpAnnotation,oligoSnpSet-method
Keywords: methods manip
Description: Retrieves SNP-level annotation
URL: ../../../library/SNPchip/html/getSnpAnnotation.html

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

Entry: initialize-methods
Aliases: initialize-methods initialize,oligoSnpSet-method
Keywords: methods
Description: Generates instances of SnpSet objects
URL: ../../../library/SNPchip/html/initialize-methods.html

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

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

Entry: position-methods
Aliases: position position,AnnotatedDataFrame-method position,SnpLevelSet-method
Keywords: methods manip
Description: Physical position of SNP on chromosome
URL: ../../../library/SNPchip/html/position.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
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: 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: unsplitSnpSet
Aliases: unsplitSnpSet unsplitSnpSet-methods unsplitSnpSet,list,AnnotatedDataFrame-method
Keywords: manip
Description: Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.
URL: ../../../library/SNPchip/html/unsplitSnpSet.html

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