RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

Author
Saskia Freytag
Date of publication
None
Maintainer
Saskia Freytag <freytag.s@wehi.edu.au>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

assessQuality
Quality assessment for cleaning procedures.
background
Randomly choose background genes.
calculateThreshold
Calculates the correlation threshold.
compareRanks
Compare ranking of known reference gene pairs.
correlationPlot
Correlation plot to compare estimated correlations with true...
ECDFPlot
Plot empirical cumulative distribution function for...
eigenvaluePlot
Plot eigenvalues of SVD of the negtaive controls.
empNegativeControls
Empirically choose negative control genes.
findIQR
Find the inter quantile range.
findMinmaxSamples
Find minimum and maximum samples in gene expression data.
findWeights
Finds weights of each level of a factor.
funcPara
Function to optimize parameters in parallel.
funcThresh
Function to calculate correlation threshold in parallel.
genePlot
Plot of means and inter-quantile ranges of all genes.
histogramPlot
Plot histogram of correlations.
is.optimizeParameters
Checking 'optimizeParameters' class.
is.simulateGEdata
Checking 'simulateGEdata' class.
makePosSemiDef
Makes square matrices positive semi-definite.
makeRankedList
Make ranked list of correlations.
mashUp
Joining two correlation matrices by diagonal.
optimizeParameters
Optimize parameters of removal of unwanted variation.
PCAPlot
Plot principle component analysis for gene expression data.
plotDesign
Plot nested design structure.
plot.optimizeParameters
Plots an object of class 'optimizeParameters'.
plotThreshold
Plots an object of class 'Threshold'.
print.simulateGEdata
Print an object of class 'simualteGEdata'.
prioritise
Prioritising candidate genes.
RLEPlot
Plots different versions of relative log expression plots
RUVcorr
Removal of unwanted variation for gene-gene correlations.
RUVNaiveRidge
Removal of unwanted variation for gene correlations.
simulateGEdata
Simulate gene expression data.
splitByFactor
Splitting a data set by a particular factor.
wcor
Calculate weighted correlations.

Files in this package

RUVcorr/DESCRIPTION
RUVcorr/NAMESPACE
RUVcorr/R
RUVcorr/R/ECDFPlot.R
RUVcorr/R/PCAPlot.R
RUVcorr/R/RLEPlot.R
RUVcorr/R/RUVNaiveRidge.R
RUVcorr/R/RUVcorr.R
RUVcorr/R/assessQuality.R
RUVcorr/R/background.R
RUVcorr/R/calculateThreshold.R
RUVcorr/R/compareRanks.R
RUVcorr/R/correlationPlot.R
RUVcorr/R/eigenvaluePlot.R
RUVcorr/R/empNegativeControls.R
RUVcorr/R/findIQR.R
RUVcorr/R/findMinmaxSamples.R
RUVcorr/R/findWeights.R
RUVcorr/R/funcPara.R
RUVcorr/R/funcThresh.R
RUVcorr/R/genePlot.R
RUVcorr/R/histogramPlot.R
RUVcorr/R/is.optimizeParameters.R
RUVcorr/R/is.simulateGEdata.R
RUVcorr/R/makePosSemiDef.r
RUVcorr/R/makeRankedList.R
RUVcorr/R/mashUp.R
RUVcorr/R/optimizeParameters.R
RUVcorr/R/plot.optimizeParameters.r
RUVcorr/R/plotDesign.R
RUVcorr/R/plotThreshold.R
RUVcorr/R/print.simulateGEdata.R
RUVcorr/R/prioritising.r
RUVcorr/R/simulateGEdata.R
RUVcorr/R/splitByFactor.R
RUVcorr/R/wcor.R
RUVcorr/build
RUVcorr/build/vignette.rds
RUVcorr/inst
RUVcorr/inst/NEWS.Rd
RUVcorr/inst/doc
RUVcorr/inst/doc/RUVcorrVignetteNew.R
RUVcorr/inst/doc/RUVcorrVignetteNew.Rnw
RUVcorr/inst/doc/RUVcorrVignetteNew.pdf
RUVcorr/man
RUVcorr/man/ECDFPlot.Rd
RUVcorr/man/PCAPlot.Rd
RUVcorr/man/RLEPlot.Rd
RUVcorr/man/RUVNaiveRidge.Rd
RUVcorr/man/RUVcorr.Rd
RUVcorr/man/assessQuality.Rd
RUVcorr/man/background.Rd
RUVcorr/man/calculateThreshold.Rd
RUVcorr/man/compareRanks.Rd
RUVcorr/man/correlationPlot.Rd
RUVcorr/man/eigenvaluePlot.Rd
RUVcorr/man/empNegativeControls.Rd
RUVcorr/man/findIQR.Rd
RUVcorr/man/findMinmaxSamples.Rd
RUVcorr/man/findWeights.Rd
RUVcorr/man/funcPara.Rd
RUVcorr/man/funcThresh.Rd
RUVcorr/man/genePlot.Rd
RUVcorr/man/histogramPlot.Rd
RUVcorr/man/is.optimizeParameters.Rd
RUVcorr/man/is.simulateGEdata.Rd
RUVcorr/man/makePosSemiDef.Rd
RUVcorr/man/makeRankedList.Rd
RUVcorr/man/mashUp.Rd
RUVcorr/man/optimizeParameters.Rd
RUVcorr/man/plot.optimizeParameters.Rd
RUVcorr/man/plotDesign.Rd
RUVcorr/man/plotThreshold.Rd
RUVcorr/man/print.simulateGEdata.Rd
RUVcorr/man/prioritise.Rd
RUVcorr/man/simulateGEdata.Rd
RUVcorr/man/splitByFactor.Rd
RUVcorr/man/wcor.Rd
RUVcorr/vignettes
RUVcorr/vignettes/Bioc.bib
RUVcorr/vignettes/RUVcorrVignetteNew.Rnw