qusage: qusage: Quantitative Set Analysis for Gene Expression

This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

AuthorChristopher Bolen and Gur Yaari, with contributions from Juilee Thakar, Hailong Meng, Jacob Turner, Derek Blankenship, and Steven Kleinstein
Date of publicationNone
MaintainerChristopher Bolen <cbolen1@gmail.com>
LicenseGPL (>= 2)

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aggregateGeneSet Man page
BTM.geneSets Man page
calcBayesCI Man page
calcVIF Man page
combinePDFs Man page
dim,QSarray-method Man page
eset.full Man page
fluExample Man page
flu.meta Man page
fluVaccine Man page
GeneSets Man page
getXcoords Man page
head,QSarray-method Man page
ISG.geneSet Man page
makeComparison Man page
MSIG.geneSets Man page
newQSarray Man page
numFeatures Man page
numFeatures,QSarray-method Man page
numPathways Man page
numPathways,QSarray-method Man page
oneWay.pVal Man page
pdf.pVal Man page
plotCIs Man page
plotCIsGenes Man page
plotCombinedPDF Man page
plotDensityCurves Man page
plotGeneSetDistributions Man page
plot,QSarray-method Man page
print,QSarray-method Man page
qgen Man page
QSarray-class Man page
qsTable Man page
qusage Man page
read.gmt Man page
summary,QSarray-method Man page
twoCurve.pVal Man page
twoWay.pVal Man page

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