GeneSets                Example Gene Sets
QSarray-class           Class '"QSarray"'
aggregateGeneSet        Calculate Pathway Activation
calcBayesCI             Calculate pathway Confidence Intervals
calcVIF                 Calculate Variance Inflation Factor
combinePDFs             Combine PDFs from multiple QuSAGE comparisons
fluExample              Example gene expression set
fluVaccine              Gene expression sets from Flu Vaccine trials
getXcoords              Get the X coordinates for the points of the PDF
makeComparison          Compare Genes Between Two Groups
newQSarray              The qusage Array Object
pdf.pVal                Calculate p-values for gene set activity
plotCIs                 Plot Pathway Mean and Confidence Intervals
plotCIsGenes            Plot Gene Mean and Confidence Intervals
plotCombinedPDF         Plot combined PDF for an individual pathway
plotDensityCurves       Plot gene set PDFs
plotGeneSetDistributions
                        Plot gene and gene set PDFs
qgen                    Run qusage while incoprating generalized least
                        squares and linear mixed model analysis at the
                        gene level to account for repeated measures,
                        continous covariates, and confounder adjusting.
qsTable                 Summary of QSarray Results
qusage                  Run qusage on an expression dataset
read.gmt                Read in gene set information from .gmt files
