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

assessQualityQuality assessment for cleaning procedures.
backgroundRandomly choose background genes.
calculateThresholdCalculates the correlation threshold.
compareRanksCompare ranking of known reference gene pairs.
correlationPlotCorrelation plot to compare estimated correlations with true...
ECDFPlotPlot empirical cumulative distribution function for...
eigenvaluePlotPlot eigenvalues of SVD of the negtaive controls.
empNegativeControlsEmpirically choose negative control genes.
findIQRFind the inter quantile range.
findMinmaxSamplesFind minimum and maximum samples in gene expression data.
findWeightsFinds weights of each level of a factor.
funcParaFunction to optimize parameters in parallel.
funcThreshFunction to calculate correlation threshold in parallel.
genePlotPlot of means and inter-quantile ranges of all genes.
histogramPlotPlot histogram of correlations.
is.optimizeParametersChecking 'optimizeParameters' class.
is.simulateGEdataChecking 'simulateGEdata' class.
is.ThresholdChecking 'Threshold' class.
is.WeightsChecking 'Weights' class.
makePosSemiDefMakes square matrices positive semi-definite.
makeRankedListMake ranked list of correlations.
mashUpJoining two correlation matrices by diagonal.
optimizeParametersOptimize parameters of removal of unwanted variation.
PCAPlotPlot principle component analysis for gene expression data.
plotDesignPlot nested design structure.
plot.optimizeParametersPlots an object of class 'optimizeParameters'.
plotThresholdPlots an object of class 'Threshold'.
print.simulateGEdataPrint an object of class 'simualteGEdata'.
prioritisePrioritising candidate genes.
RLEPlotPlots different versions of relative log expression plots
RUVcorrRemoval of unwanted variation for gene-gene correlations.
RUVNaiveRidgeRemoval of unwanted variation for gene correlations.
simulateGEdataSimulate gene expression data.
splitByFactorSplitting a data set by a particular factor.
wcorCalculate weighted correlations.
RUVcorr documentation built on Nov. 8, 2020, 5:10 p.m.