qusage: Quantitative Set Analysis for Gene Expression

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Documentation for package ‘qusage’ version 2.41.0

• 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