$,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 |