GLOSSIResult-class      Class '"GLOSSIResult"'
GLOSSIResultCollection-class
                        Class '"GLOSSIResultCollection"'
GeneSetResult-class     Class '"GeneSetResult"'
GeneSetResultCollection-class
                        Class '"GeneSetResultCollection"'
VEGASResult-class       Class '"VEGASResult"'
VEGASResultCollection-class
                        Class '"VEGASResultCollection"'
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
                        ~~ Methods for Function 'degreesOfFreedom' ~~
exampleArrayData        SNP Array Data to Use for Gene Set Analysis
geneSetAnalysis         Data to run gene set analysis methods
geneSetName-methods     ~~ Methods for Function 'geneSetName' ~~
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
pValue-methods          ~~ Methods for Function 'pValue' ~~
plotPvals               Create a Plot of P-Values Against Number of
                        SNPs per Set for All Sets in a Collection
show                    ~~ Methods for Function 'show' in Package
                        'base' ~~
simulate_chisq          Simulate a Chi-squared Statistic from a
                        Distribution with a Specified Correlation
                        Structure
simulatedStats-methods
                        ~~ Methods for Function 'simulatedStats' ~~
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
