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.

AuthorSaskia Freytag
Date of publicationNone
MaintainerSaskia Freytag <freytag.s@wehi.edu.au>
LicenseGPL-2
Version1.6.0

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

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