Classes and Methods for high throughput SNP chip data


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Documentation for package ‘SNPchip’ version 1.2.1

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$,ParESet-method Class "ParESet"
$<-,ParESet-method Class "ParESet"
addFeatureData Method for Function addFeatureData
addFeatureData,eSet-method Method for Function addFeatureData
addFeatureData-methods Method for Function addFeatureData
alleleA Accessor for the A allele
alleleA,AnnotatedDataFrame-method Accessor for the A allele
alleleA,SnpLevelSet-method Accessor for the A allele
alleleB Accessor for the B allele
alleleB,AnnotatedDataFrame-method Accessor for the B allele
alleleB,SnpLevelSet-method Accessor for the B allele
allPlots Extracts graphical parameters to be used by all plotting devices
allPlots,ParESet-method Class "ParESet"
AnnotatedSnpCallSet-class Deprecated classes
AnnotatedSnpCopyNumberSet-class Deprecated classes
AnnotatedSnpSet-class Deprecated classes
calculateCopyNumber Extracts copy number estimates from thetas in SnpQSet object
calculateCopyNumber,SnpQSet-method Extracts copy number estimates from thetas in SnpQSet object
calculateCopyNumber-methods Extracts copy number estimates from thetas in SnpQSet object
centromere Coordinates of centromere
chromosome Accessor for chromosome SNP annotation
chromosome,AnnotatedDataFrame-method Accessor for chromosome SNP annotation
chromosome,SnpLevelSet-method Accessor for chromosome SNP annotation
chromosome-methods Accessor for chromosome SNP annotation
chromosomeAnnotation chromosome annotation
chromosomeSize Get size of chromosome in number of base pairs.
coerce,AnnotatedSnpCallSet,SnpCallSet-method Methods for Function coerce
coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method Methods for Function coerce
coerce,AnnotatedSnpSet,oligoSnpSet-method Methods for Function coerce
coerce-methods Methods for Function coerce
cytoband Start and stop sites of cytoband
dbSnpId The dbSNP identifier
dbSnpId,AnnotatedDataFrame-method The dbSNP identifier
dbSnpId,SnpLevelSet-method The dbSNP identifier
enzyme Enzyme used to digest DNA
enzyme,AnnotatedDataFrame-method Enzyme used to digest DNA
enzyme,SnpLevelSet-method Enzyme used to digest DNA
fragmentLength Accessor for the fragment length
fragmentLength,AnnotatedDataFrame-method Accessor for the fragment length
fragmentLength,SnpLevelSet-method Accessor for the fragment length
getPar Computes default graphical parameters
getPar,SnpLevelSet-method Computes default graphical parameters
getPar-methods Computes default graphical parameters
getSnpAnnotation Retrieves SNP-level annotation
getSnpAnnotation,oligoSnpSet-method Retrieves SNP-level annotation
getSnpAnnotation,SnpCallSet-method Retrieves SNP-level annotation
getSnpAnnotation,SnpCopyNumberSet-method Retrieves SNP-level annotation
getSnpAnnotation,SnpLevelSet-method Retrieves SNP-level annotation
hapmap Data from the hapmap project
initialize,oligoSnpSet-method Generates instances of SnpSet objects
initialize,ParESet-method Class "ParESet"
initialize,ParSnpCallSet-method Class "ParSnpCallSet"
initialize,ParSnpCopyNumberSet-method Class "ParSnpCopyNumberSet"
initialize,ParSnpSet-method Class "ParSnpSet"
initialize-methods Generates instances of SnpSet objects
ParESet-class Class "ParESet"
ParSnpCallSet-class Class "ParSnpCallSet"
ParSnpCopyNumberSet-class Class "ParSnpCopyNumberSet"
ParSnpSet-class Class "ParSnpSet"
plotCytoband Plots cytoband for one chromosome
plotSnp Plots copy number and genotype calls against physical position
plotSnp,ParESet,ANY-method Plots copy number and genotype calls against physical position
plotSnp,ParSnpCallSet,SnpCallSet-method Plots copy number and genotype calls against physical position
plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method Plots copy number and genotype calls against physical position
plotSnp,ParSnpSet,oligoSnpSet-method Plots copy number and genotype calls against physical position
position Physical position of SNP on chromosome
position,AnnotatedDataFrame-method Physical position of SNP on chromosome
position,SnpLevelSet-method Physical position of SNP on chromosome
sample.snpset Example object of class oligoSnpSet
selectSomeIndex Method from Biobase for selecting indices
selectSomeIndex,data.frame-method Method from Biobase for selecting indices
show,oligoSnpSet-method show methods
show-methods show methods
showSummary Displays descriptive statistics for a sample.
smoothSnp A simple nonparametric smoother for genotype and copy number
smoothSnp,oligoSnpSet-method A simple nonparametric smoother for genotype and copy number
snpPar Accessor for graphical parameters
snpPar,ParESet-method Class "ParESet"
snpPar<-,ParESet-method Class "ParESet"
summary,AnnotatedSnpSet-method Methods for Function summary
summary,ANY-method Methods for Function summary
summary,oligoSnpSet-method Methods for Function summary
summary,SnpCallSet-method Methods for Function summary
summary-methods Methods for Function summary
unsplitSnpSet Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.
unsplitSnpSet,list,AnnotatedDataFrame-method Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.
unsplitSnpSet-methods Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.
updateObject,AnnotatedSnpSet-method updateObject methods
updateObject,oligoSnpSet-method updateObject methods