| 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"' |