# qusage: Quantitative Set Analysis for Gene Expression

## Documentation for package ‘qusage’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregateGeneSet | Calculate Pathway Activation
calcBayesCI | Calculate pathway Confidence Intervals
calcVIF | Calculate Variance Inflation Factor
dim-method | Class '"QSarray"'
eset | Example gene expression set
fluExample | Example gene expression set
getXcoords | Get the X coordinates for the points of the PDF
head-method | Class '"QSarray"'
ISG.geneSet | Example gene set containing IFN stimulated genes
makeComparison | Compare Genes Between Two Groups
MSIG.geneSets | MSigDB's Canonical Pathways gene set database.
newQSarray | The qusage Array Object
numFeatures | Class '"QSarray"'
numFeatures-method | Class '"QSarray"'
numPathways | Class '"QSarray"'
numPathways-method | Class '"QSarray"'
oneWay.pVal | Calculate p-values for gene set activity
pdf.pVal | Calculate p-values for gene set activity
plot-method | Class '"QSarray"'
plotCIs | Plot Pathway Mean and Confidence Intervals
plotCIsGenes | Plot Gene Mean and Confidence Intervals
plotDensityCurves | Plot gene set PDFs
plotGeneSetDistributions | Plot gene and gene set PDFs
print-method | Class '"QSarray"'
QSarray-class | Class '"QSarray"'
qsTable | Summary of QSarray Results
qusage | Run qusage on an expression dataset
read.gmt | Read in gene set information from .gmt files
resp | Example gene expression set
summary-method | Class '"QSarray"'
twoCurve.pVal | Calculate p-values for gene set activity
twoWay.pVal | Calculate p-values for gene set activity