89 gsora and gsea.

[jmitchell81]

• getPatternHallmarks changed to getPatternGeneSets
• getPatternGeneSets can conduct gene set enrichment analysis, ranking features by pattern amplitude, or gene set overrepresentation analysis, for occurrence of gene sets within pattern marker lists.
• removes usage of msigdbr to query the hallmark gene sets. Gene set inputs are now provided as lists.
• function to plot the gene set test result updated to plot either enrichment or overrepresentation under the same framework, change the title to reflect which test was used, and change the p-value threshold used to decide which gene sets are rendered on the plot.
• implements unit tests for the capability to generate gene set test results for enrichment and overrepresentation tests on the GIST data and tests the capability to generate a ggplot object from the plotting function for both test types.