qusage: qusage: Quantitative Set Analysis for Gene Expression
Version 2.10.0

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
Bioconductor views GeneSetEnrichment Microarray RNASeq Software
Date of publicationNone
MaintainerChristopher Bolen <cbolen1@gmail.com>
LicenseGPL (>= 2)
Version2.10.0
URL http://clip.med.yale.edu/qusage
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("qusage")

Popular man pages

aggregateGeneSet: Calculate Pathway Activation
calcVIF: Calculate Variance Inflation Factor
eset.full: Example gene expression set
GeneSets: Example Gene Sets
plotCIsGenes: Plot Gene Mean and Confidence Intervals
qgen: Run qusage while incoprating generalized least squares and...
read.gmt: Read in gene set information from .gmt files
See all...

All man pages Function index File listing

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

Functions

BTM.geneSets Man page
GeneSets Man page
ISG.geneSet Man page
MSIG.geneSets Man page
Ni Source code
QSarray-class Man page
absoluteTest Source code
absoluteTest.genePvals Source code
absoluteTest.genePvalsFAST Source code
aggregateGeneSet Man page Source code
calcBayesCI Man page Source code
calcIndividualExpressions Source code
calcPCor Source code
calcVIF Man page Source code
calculate_bayesGHelper Source code
combinePDFs Man page Source code
compareTwoDistsFaster Source code
dim,QSarray-method Man page
eset.full Man page
filterGenes Source code
flu.meta Man page
fluExample Man page
fluVaccine Man page
getExAbs Source code
getXcoords Man page Source code
head,QSarray-method Man page
homogeneityScore Source code
makeComparison Man page Source code
multi_conv Source code
newQSarray Man page Source code
nonsingular.check Source code
numFeatures Man page
numFeatures,QSarray-method Man page
numPathways Man page
numPathways,QSarray-method Man page
oneWay.pVal Man page Source code
pdf.pVal Man page Source code
pdfScaleFactor Source code
plot,QSarray-method Man page
plotCIs Man page Source code
plotCIsGenes Man page Source code
plotCombinedPDF Man page Source code
plotDensityCurves Man page Source code
plotGeneSetDistributions Man page Source code
print,QSarray-method Man page
qgen Man page Source code
qsTable Man page Source code
qusage Man page Source code
qusage.single Source code
read.gmt Man page Source code
summary,QSarray-method Man page
twoCurve.pVal Man page Source code
twoWay.pVal Man page Source code
weighted_conv Source code

Files

DESCRIPTION
NAMESPACE
R
R/CombinePDF.R
R/QSarray.R
R/QSarray_plotFns.R
R/QgenFunctions.R
R/qusage.R
build
build/vignette.rds
data
data/GeneSets.RData
data/datalist
data/fluExample.RData
data/fluVaccine.RData
inst
inst/CITATION
inst/doc
inst/doc/qusage.R
inst/doc/qusage.Rnw
inst/doc/qusage.pdf
man
man/GeneSets.Rd
man/QSarray-class.Rd
man/aggregateGeneSet.Rd
man/calcBayesCI.Rd
man/calcVIF.Rd
man/combinePDFs.Rd
man/eset.full.Rd
man/fluVaccine.Rd
man/getXcoords.Rd
man/makeComparison.Rd
man/newQSarray.Rd
man/pVal.Rd
man/plotCIs.Rd
man/plotCIsGenes.Rd
man/plotCombinedPDF.Rd
man/plotDensityCurves.Rd
man/plotGeneSetDistributions.Rd
man/qgen.Rd
man/qsTable.Rd
man/qusage.Rd
man/read.gmt.Rd
vignettes
vignettes/qusage.Rnw
qusage documentation built on May 20, 2017, 9:35 p.m.