Classes and Methods for high throughput SNP chip data

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Documentation for package ‘SNPchip’ version 1.14.0

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$-method Class "ParESet"
$<--method Class "ParESet"
addFeatureData Method for Function addFeatureData
addFeatureData-method Method for Function addFeatureData
addFeatureData-methods Method for Function addFeatureData
alleleA Accessor for the A allele
alleleA-method Accessor for the A allele
alleleB Accessor for the B allele
alleleB-method Accessor for the B allele
centromere Coordinates of centromere
chromosome Accessors for feature-level SNP annotation
chromosome-method Accessors for feature-level SNP annotation
chromosome-methods Accessors for feature-level SNP annotation
chromosomeAnnotation chromosome annotation
chromosomeSize Size of chromosome in number of base pairs.
coerce-method Methods for Function coerce
coerce-methods Methods for Function coerce
crlmmOut A data object created by the oligo vignette
cytoband Start and stop sites of cytoband
dbSnpId The dbSNP identifier
dbSnpId-method The dbSNP identifier
enzyme Enzyme used to digest DNA
enzyme-method Enzyme used to digest DNA
fragmentLength Accessor for the fragment length
fragmentLength-method Accessor for the fragment length
getPar Adds graphical parameters for plotting SNP data
getPar-method Adds graphical parameters for plotting SNP data
hapmap Data from the hapmap project
hmmPredict Accessor for HMM output
hmmPredict-method Class "ParESet"
initialize-method Class "ParESet"
initialize-method Class "ParSnpCallSet"
initialize-method Class "ParSnpCopyNumberSet"
initialize-method Class "ParSnpSet"
integer2chromosome Converts integer representation of chromosome number back to letter
ParESet-class Class "ParESet"
ParSnpCallSet-class Class "ParSnpCallSet"
ParSnpCopyNumberSet-class Class "ParSnpCopyNumberSet"
ParSnpSet-class Class "ParSnpSet"
plot Plots copy number and genotype calls against physical position
plot-method Plots copy number and genotype calls against physical position
plotCytoband Plots idiogram for one chromosome
plotPredictions Plots the predictions from the HMM
plotSnp Plots copy number and genotype calls against physical position
plotSnp-method Class "ParESet"
plotSnp-method Plots copy number and genotype calls against physical position
position Accessors for feature-level SNP annotation
position-method Accessors for feature-level SNP annotation
position-methods Accessors for feature-level SNP annotation
sample.snpset Example object of class oligoSnpSet
show-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-method A simple nonparametric smoother for genotype and copy number
snpPar Accessor for graphical parameters
snpPar-method Class "ParESet"
snpPar<- Accessor for graphical parameters
snpPar<--method Class "ParESet"
snpset Accessor for SNP data
snpset-method Class "ParESet"
summary-method Summary statistics for various SNP classes that extend eSet
summary-methods Summary statistics for various SNP classes that extend eSet
updateObject-method updateObject methods