| 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 |
| chromosome2numeric |
Converts chromosome to numeric |
| chromosomeAnnotation |
chromosome annotation |
| chromosomeSize |
Get 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" |
| 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 |