# qusage: Quantitative Set Analysis for Gene Expression

## Documentation for package ‘qusage’ version 2.20.0

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

## Help Pages

aggregateGeneSet | Calculate Pathway Activation
BTM.geneSets | Example Gene Sets
calcBayesCI | Calculate pathway Confidence Intervals
calcVIF | Calculate Variance Inflation Factor
combinePDFs | Combine PDFs from multiple QuSAGE comparisons
dim-method | Class '"QSarray"'
eset.full | Example gene expression set
flu.meta | Example gene expression set
fluExample | Example gene expression set
fluVaccine | Gene expression sets from Flu Vaccine trials
GeneSets | Example Gene Sets
getXcoords | Get the X coordinates for the points of the PDF
head-method | Class '"QSarray"'
ISG.geneSet | Example Gene Sets
makeComparison | Compare Genes Between Two Groups
MSIG.geneSets | Example Gene Sets
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
plotCombinedPDF | Plot combined PDF for an individual pathway
plotDensityCurves | Plot gene set PDFs
plotGeneSetDistributions | Plot gene and gene set PDFs
print-method | Class '"QSarray"'
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.
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
summary-method | Class '"QSarray"'
twoCurve.pVal | Calculate p-values for gene set activity
twoWay.pVal | Calculate p-values for gene set activity