Entry: AnnotatedSnpCallSet-class
Aliases: AnnotatedSnpCallSet-class alleleA,SnpCallSet-class alleleB,SnpCallSet-class chromosomeAnnotation,AnnotatedSnpCallSet-method chromosomeAnnotation<-,AnnotatedSnpCallSet,data.frame-method
Keywords: classes
Description: Class "AnnotatedSnpCallSet"
URL: ../../../library/SNPchip/html/AnnotatedSnpCallSet-class.html

Entry: AnnotatedSnpCopyNumberSet-class
Aliases: AnnotatedSnpCopyNumberSet-class alleleA,SnpCopyNumberSet-method alleleA,AnnotatedSnpCopyNumberSet-method alleleB,AnnotatedSnpCopyNumberSet-method alleleB,SnpCopyNumberSet-method coerce,AnnotatedSnpCopyNumberSet,AnnotatedSnpSet-method chromosome,AnnotatedSnpCopyNumberSet-method chromosomeAnnotation,AnnotatedSnpCopyNumberSet-method chromosomeAnnotation<-,AnnotatedSnpCopyNumberSet,data.frame-method dbSnpId,AnnotatedSnpCopyNumberSet-method enzyme,AnnotatedSnpCopyNumberSet-method fragmentLength,AnnotatedSnpCopyNumberSet-method plotSnp,AnnotatedSnpCopyNumberSet-method position,AnnotatedSnpCopyNumberSet-method
Keywords: classes
Description: Class "AnnotatedSnpCopyNumberSet"
URL: ../../../library/SNPchip/html/AnnotatedSnpCopyNumberSet-class.html

Entry: AnnotatedSnpSet-class
Aliases: AnnotatedSnpSet-class alleleA,AnnotatedSnpSet-method alleleB,AnnotatedSnpSet-method coerce,AnnotatedSnpSet,AnnotatedSnpCopyNumberSet-method chromosome,AnnotatedSnpSet-method chromosomeAnnotation,AnnotatedSnpSet-method chromosomeAnnotation<-,AnnotatedSnpSet,data.frame-method dbSnpId,AnnotatedSnpSet-method enzyme,AnnotatedSnpSet-method fData,AnnotatedSnpSet-method fragmentLength,AnnotatedSnpSet-method plotCytoband,AnnotatedSnpSet-method plotSnp,AnnotatedSnpSet-method position,AnnotatedSnpSet-method smoothSnp,AnnotatedSnpSet-method
Keywords: classes
Description: Class "AnnotatedSnpSet"
URL: ../../../library/SNPchip/html/AnnotatedSnpSet-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: alleleA
Aliases: alleleA alleleA,AnnotatedDataFrame-method alleleA,oligoSnpSet-method alleleA,SnpCallSet-method
Keywords: methods
Description: Accessor for the A allele
URL: ../../../library/SNPchip/html/alleleA.html

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

Entry: annSnpset
Aliases: annSnpset
Keywords: datasets
Description: AnnotatedSnpSet object
URL: ../../../library/SNPchip/html/annSnpset.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,oligoSnpSet-method chromosome,SnpCallSet-method chromosome,SnpCopyNumberSet-method chromosome,AnnotatedDataFrame-method
Keywords: methods manip
Description: Accessor for chromosome SNP annotation
URL: ../../../library/SNPchip/html/chromosome.html

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

Entry: copyNumber-methods
Aliases: copyNumber-methods copyNumber,SnpQSet-method
Keywords: methods manip
Description: Extracts copy number estimates
URL: ../../../library/SNPchip/html/copyNumber.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,SnpCallSet-method dbSnpId,SnpCopyNumberSet-method dbSnpId,AnnotatedDataFrame-method dbSnpId,oligoSnpSet-method
Keywords: manip
Description: The dbSNP identifier.
URL: ../../../library/SNPchip/html/dbSnpId.html

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

Entry: fData
Aliases: fData fData,eSet-method fData<- fData<-,eSet,data.frame-method
Keywords: manip
Description: Accessor for the data.frame in featureData
URL: ../../../library/SNPchip/html/fData.html

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

Entry: getSnpAnnotation
Aliases: getSnpAnnotation getSnpAnnotation,eSet-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,SnpCallSet-method initialize,AnnotatedSnpCallSet-method initialize,SnpCopyNumberSet-method initialize,AnnotatedSnpCopyNumberSet-method initialize,oligoSnpSet-method initialize,AnnotatedSnpSet-method initialize,AnnotatedSnpSetList-method
Keywords: methods
Description: Generates instances of SnpSet objects
URL: ../../../library/SNPchip/html/initialize-methods.html

Entry: plotCytoband
Aliases: plotCytoband
Keywords: aplot
Description: Adds cytoband to plot.
URL: ../../../library/SNPchip/html/plotCytoband.html

Entry: plotSnp
Aliases: plotSnp
Keywords: hplot
Description: Plots copy number and genotype calls.
URL: ../../../library/SNPchip/html/plotSnp.html

Entry: position-methods
Aliases: position position,SnpCallSet-method position,SnpCopyNumberSet-method position,AnnotatedDataFrame-method position,oligoSnpSet-method
Keywords: methods manip
Description: Physical position of SNP on chromosome
URL: ../../../library/SNPchip/html/position.html

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

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

Entry: unsplitS4
Aliases: unsplitS4
Keywords: manip
Description: Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.
URL: ../../../library/SNPchip/html/unsplitS4.html
