qusage: Quantitative Set Analysis for Gene Expression


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Documentation for package ‘qusage’ version 1.6.0

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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