$-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 representation |
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 |