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| calcTNullFast | Compute Null T Distribution for Each Gene |
| calcTStatFast | Compute T-Statistics and Corresponding P-Values |
| calculate.GSEA | Calculate 2-sided statistics based on the GSEA algorithm |
| calculate.NEk | Calculate the NTk and NEk statistics |
| calculate.NGSk | Calculate NGSk (NTk-like) statistics with gene label permutation |
| calculate.NTk | Calculate the NTk and NEk statistics |
| estimateNumPerm | Compute the Number of Unique Permutations for a Phenotype Vector |
| G | Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway |
| getPathwayStatistics | Give the statistics for the probe sets in a pathway |
| getPathwayStatistics.NGSk | Give the statistics for the probe sets in a pathway |
| gmtToG | Import gene sets stored in GMT, GMX, GRP, and XML file formats |
| gmxToG | Import gene sets stored in GMT, GMX, GRP, and XML file formats |
| grpToG | Import gene sets stored in GMT, GMX, GRP, and XML file formats |
| importGeneSets | Import gene sets stored in GMT, GMX, GRP, and XML file formats |
| MuscleExample | Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway |
| phenotype | Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway |
| rankPathways | Summarizes Top Pathways from Pathway Analyses |
| rankPathways.NGSk | Summarizes Top Pathways from One of the Pathway Analyses |
| runSigPathway | Perform pathway analysis |
| selectGeneSets | Select gene sets to be analyzed in pathway analysis |
| tab | Subset of Inflammatory Myopathy Dataset to Demonstrate sigPathway |
| writeSigPathway | Write results of pathway analysis to HTML format |
| writeSP | Write results of pathway analysis to HTML format |
| xmlToG | Import gene sets stored in GMT, GMX, GRP, and XML file formats |