centromere |
Coordinates of centromere |
chromosome |
Accessors for feature-level SNP annotation |
chromosome,AnnotatedDataFrame-method |
Accessors for feature-level SNP annotation |
chromosome,oligoSnpSet-method |
Accessors for feature-level SNP annotation |
chromosome,SnpCallSet-method |
Accessors for feature-level SNP annotation |
chromosome,SnpCopyNumberSet-method |
Accessors for feature-level SNP annotation |
chromosome,SnpLevelSet-method |
Accessors for feature-level SNP annotation |
chromosome-methods |
Accessors for feature-level SNP annotation |
chromosome2integer |
Converts chromosome to integer or vice versa |
chromosomeAnnotation |
chromosome annotation |
chromosomeSize |
Size of chromosome in number of base pairs. |
cnConfidence,RatioSnpSet-method |
Accessors for RatioSnpSet objects |
cnConfidence<-,RatioSnpSet,matrix-method |
Accessors for RatioSnpSet objects |
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,oligoSnpSet,SnpCallSet-method |
Methods for Function coerce |
coerce,oligoSnpSet,SnpCopyNumberSet-method |
Methods for Function coerce |
coerce-methods |
Methods for Function coerce |
copyNumber,RatioSnpSet-method |
Accessors for RatioSnpSet objects |
copyNumber<-,RatioSnpSet,matrix-method |
Accessors for RatioSnpSet objects |
crlmmOut |
A data object created by the oligo vignette |
cytoband |
Start and stop sites of cytoband |
ParESet-class |
Class "ParESet" |
ParSnpCallSet-class |
Class "ParSnpCallSet" |
ParSnpCopyNumberSet-class |
Class "ParSnpCopyNumberSet" |
ParSnpSet-class |
Class "ParSnpSet" |
plot,ParSnpCallSet,SnpCallSet-method |
Plots copy number and genotype calls against physical position |
plot,ParSnpCopyNumberSet,SnpCopyNumberSet-method |
Plots copy number and genotype calls against physical position |
plot,ParSnpSet,oligoSnpSet-method |
Plots copy number and genotype calls against physical position |
plot,SnpLevelSet-method |
Plots copy number and genotype calls against physical position |
plotCytoband |
Plots cytoband for one chromosome |
plotPredictions |
Plots the predictions from the HMM |
plotSnp |
Plots copy number and genotype calls against physical position |
plotSnp,ParESet,SnpLevelSet-method |
Class "ParESet" |
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 |
plotSnp,SnpLevelSet-method |
Plots copy number and genotype calls against physical position |
position |
Accessors for feature-level SNP annotation |
position,AnnotatedDataFrame-method |
Accessors for feature-level SNP annotation |
position,oligoSnpSet-method |
Accessors for feature-level SNP annotation |
position,SnpCallSet-method |
Accessors for feature-level SNP annotation |
position,SnpCopyNumberSet-method |
Accessors for feature-level SNP annotation |
position,SnpLevelSet-method |
Accessors for feature-level SNP annotation |
position-methods |
Accessors for feature-level SNP annotation |
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,ParESet-method |
show methods |
show,ParSnpCallSet-method |
show methods |
show,ParSnpCopyNumberSet-method |
show methods |
show,ParSnpSet-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" |
snpset |
Accessor for SNP data |
snpset,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 |