qusage: Quantitative Set Analysis for Gene Expression


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Documentation for package ‘qusage’ version 2.4.0

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