qusage: qusage: Quantitative Set Analysis for Gene Expression

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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)

Author
Christopher Bolen and Gur Yaari, with contributions from Juilee Thakar, Hailong Meng, Jacob Turner, Derek Blankenship, and Steven Kleinstein
Date of publication
None
Maintainer
Christopher Bolen <cbolen1@gmail.com>
License
GPL (>= 2)
Version
2.6.0
URLs

View on Bioconductor

Man pages

aggregateGeneSet
Calculate Pathway Activation
calcBayesCI
Calculate pathway Confidence Intervals
calcVIF
Calculate Variance Inflation Factor
combinePDFs
Combine PDFs from multiple QuSAGE comparisons
eset.full
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
makeComparison
Compare Genes Between Two Groups
newQSarray
The qusage Array Object
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
pVal
Calculate p-values for gene set activity
qgen
Run qusage while incoprating generalized least squares and...
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

Files in this package

qusage/DESCRIPTION
qusage/NAMESPACE
qusage/R
qusage/R/CombinePDF.R
qusage/R/QSarray.R
qusage/R/QSarray_plotFns.R
qusage/R/QgenFunctions.R
qusage/R/qusage.R
qusage/build
qusage/build/vignette.rds
qusage/data
qusage/data/GeneSets.RData
qusage/data/datalist
qusage/data/fluExample.RData
qusage/data/fluVaccine.RData
qusage/inst
qusage/inst/CITATION
qusage/inst/doc
qusage/inst/doc/qusage.R
qusage/inst/doc/qusage.Rnw
qusage/inst/doc/qusage.pdf
qusage/man
qusage/man/GeneSets.Rd
qusage/man/QSarray-class.Rd
qusage/man/aggregateGeneSet.Rd
qusage/man/calcBayesCI.Rd
qusage/man/calcVIF.Rd
qusage/man/combinePDFs.Rd
qusage/man/eset.full.Rd
qusage/man/fluVaccine.Rd
qusage/man/getXcoords.Rd
qusage/man/makeComparison.Rd
qusage/man/newQSarray.Rd
qusage/man/pVal.Rd
qusage/man/plotCIs.Rd
qusage/man/plotCIsGenes.Rd
qusage/man/plotCombinedPDF.Rd
qusage/man/plotDensityCurves.Rd
qusage/man/plotGeneSetDistributions.Rd
qusage/man/qgen.Rd
qusage/man/qsTable.Rd
qusage/man/qusage.Rd
qusage/man/read.gmt.Rd
qusage/vignettes
qusage/vignettes/qusage.Rnw