assocPvalBySetPlot | Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set |
createArrayData | Create a GRanges Object for a GWAS data.frame |
degreesOfFreedom | ~~ Methods for Function 'degreesOfFreedom' ~~ |
degreesOfFreedom-method | ~~ Methods for Function 'degreesOfFreedom' ~~ |
degreesOfFreedom-methods | ~~ Methods for Function 'degreesOfFreedom' ~~ |
exampleArrayData | SNP Array Data to Use for Gene Set Analysis |
geneSetAnalysis | Data to run gene set analysis methods |
geneSetName | ~~ Methods for Function 'geneSetName' ~~ |
geneSetName-method | ~~ Methods for Function 'geneSetName' ~~ |
geneSetName-methods | ~~ Methods for Function 'geneSetName' ~~ |
GeneSetResult-class | Class '"GeneSetResult"' |
GeneSetResultCollection-class | Class '"GeneSetResultCollection"' |
geneSets | Gene Set Collection object |
geneToSNPList | Translate a List of Gene Ids to Their Corresponding SNP Ids |
glossi | Calculate a Chi-squared Statistic and P-Value for Independent Items of a Set Using the GLOSSI Method |
glossiMarginal | Calculate a Chi-squared Statistic and P-Value for Items in a Set |
GLOSSIResult-class | Class '"GLOSSIResult"' |
GLOSSIResultCollection-class | Class '"GLOSSIResultCollection"' |
plotPvals | Create a Plot of P-Values Against Number of SNPs per Set for All Sets in a Collection |
pValue | ~~ Methods for Function 'pValue' ~~ |
pValue-method | ~~ Methods for Function 'pValue' ~~ |
pValue-methods | ~~ Methods for Function 'pValue' ~~ |
show | ~~ Methods for Function 'show' in Package 'base' ~~ |
show-method | ~~ Methods for Function 'show' in Package 'base' ~~ |
show-methods | ~~ Methods for Function 'show' in Package 'base' ~~ |
simulatedStats | ~~ Methods for Function 'simulatedStats' ~~ |
simulatedStats-method | ~~ Methods for Function 'simulatedStats' ~~ |
simulatedStats-methods | ~~ Methods for Function 'simulatedStats' ~~ |
simulate_chisq | Simulate a Chi-squared Statistic from a Distribution with a Specified Correlation Structure |
statistic | ~~ Methods for Function 'statistic' ~~ |
statistic-method | ~~ Methods for Function 'statistic' ~~ |
statistic-methods | ~~ Methods for Function 'statistic' ~~ |
vegas | Calculate the P-Value for a Set Using the VEGAS Method |
vegasMarginal | Calculate the P-Value for a Set Using the VEGAS Method |
VEGASResult-class | Class '"VEGASResult"' |
VEGASResultCollection-class | Class '"VEGASResultCollection"' |