qusage: Quantitative Set Analysis for Gene Expression

Documentation for package ‘qusage’ version 1.2.0

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