variancePartition: Quantify and interpret divers of variation in multilevel gene expression experiments
Version 1.6.0

Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.

Browse man pages Browse package API and functions Browse package files

AuthorGabriel E. Hoffman
Bioconductor views GeneExpression RNASeq Regression Software
Date of publicationNone
MaintainerGabriel E. Hoffman <gabriel.hoffman@mssm.edu>
LicenseGPL (>= 2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("variancePartition")

Man pages

as.matrix-varPartResults-method: Convert to matrix
calcVarPart-method: Compute variance statistics
canCorPairs: canCorPairs
colinearityScore: Collinearity score
ESS-method: Effective sample size
extractVarPart: Extract variance statistics
fitExtractVarPartModel-method: Fit linear (mixed) model, report variance fractions
fitVarPartModel-method: Fit linear (mixed) model
getVarianceComponents: Extract variance terms
ggColorHue: Default colors for ggplot
plotCorrMatrix: plotCorrMatrix
plotCorrStructure: plotCorrStructure
plotPercentBars: Bar plot of variance fractions
plotStratify: plotStratify
plotStratifyBy: plotStratifyBy
plotVarPart-method: Violin plot of variance fractions
residuals-VarParFitList-method: Residuals from model fit
sortCols-method: Sort variance partition statistics
varPartConfInf: Linear mixed model confidence intervals
varPartData: Simulation dataset for examples

Functions

ESS Man page
ESS,lmerMod-method Man page
as.matrix Man page
as.matrix,varPartResults-method Man page
calcVarPart Man page
calcVarPart,lm-method Man page
calcVarPart,lmerMod-method Man page
canCorPairs Man page Source code
colinearityScore Man page Source code
exprIter Source code
extractVarPart Man page Source code
fitExtractVarPartModel Man page Source code
fitExtractVarPartModel,EList-method Man page
fitExtractVarPartModel,ExpressionSet-method Man page
fitExtractVarPartModel,data.frame-method Man page
fitExtractVarPartModel,matrix-method Man page
fitVarPartModel Man page Source code
fitVarPartModel,EList-method Man page
fitVarPartModel,ExpressionSet-method Man page
fitVarPartModel,data.frame-method Man page
fitVarPartModel,matrix-method Man page
geneCounts Man page
geneExpr Man page
getAdjustVariables Source code
getVarianceComponents Man page Source code
get_denom Source code
ggColorHue Man page Source code
heatmap.3 Source code
info Man page
isMultipleVaryingCoefficientTerms Source code
isVaryingCoefficientModel Source code
plotCorrMatrix Man page Source code
plotCorrStructure Man page Source code
plotPercentBars Man page Source code
plotStratify Man page Source code
plotStratifyBy Man page Source code
plotVarPart Man page Source code
plotVarPart,data.frame-method Man page
plotVarPart,matrix-method Man page Man page
plotVarPart,varPartResults-method Man page Man page
residuals Man page
residuals,VarParFitList-method Man page
sMixedModelFormula Source code
sortCols Man page Source code
sortCols,data.frame-method Man page
sortCols,matrix-method Man page
sortCols,varPartResults-method Man page
varPartConfInf Man page Source code
varPartData Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ESS.R
R/calcVarPart.R
R/canCorPairs.R
R/checkModelStatus.R
R/confidenceIntervals.R
R/extractVarPart.R
R/fitModels.R
R/fitVarTest.R
R/heatmap.R
R/misc.R
R/plotCorrMatrix.R
R/plotCorrStructure.R
R/plotStratifyBy.R
R/plots.R
R/sortCols.R
TODO
build
build/vignette.rds
data
data/varPartData.rda
inst
inst/CITATION
inst/doc
inst/doc/additional_visualization.R
inst/doc/additional_visualization.Rnw
inst/doc/additional_visualization.pdf
inst/doc/variancePartition.R
inst/doc/variancePartition.Rnw
inst/doc/variancePartition.pdf
man
man/ESS-method.Rd
man/as.matrix-varPartResults-method.Rd
man/calcVarPart-method.Rd
man/canCorPairs.Rd
man/colinearityScore.Rd
man/extractVarPart.Rd
man/fitExtractVarPartModel-method.Rd
man/fitVarPartModel-method.Rd
man/getVarianceComponents.Rd
man/ggColorHue.Rd
man/plotCorrMatrix.Rd
man/plotCorrStructure.Rd
man/plotPercentBars.Rd
man/plotStratify.Rd
man/plotStratifyBy.Rd
man/plotVarPart-method.Rd
man/residuals-VarParFitList-method.Rd
man/sortCols-method.Rd
man/varPartConfInf.Rd
man/varPartData.Rd
vignettes
vignettes/additional_visualization.Rnw
vignettes/library.bib
vignettes/variancePartition.Rnw
variancePartition documentation built on May 20, 2017, 9:13 p.m.