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

assessQualityQuality assessment for cleaning procedures.
backgroundRandomly choose background genes.
calculateEFDRCalculates the empricial false discovery rate.
ColantuoniAnnotationAnnotation of 266 gene expression samples collected in human...
ColantuoniDataPre-processed gene expression in the prefrontal cortex of 266...
correlationPlotCorrelation plot to compare estimated correlations with true...
ECDFPlotPlot empirical cumulative distribution function for...
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.
genePlotPlot of means and inter-quantile ranges of all genes.
histogramPlotPlot histogram of correlations.
is.optimizeParametersChecking 'optimizeParameters' class.
is.simulateGEdataChecking 'simulateGEdata' class.
makePosSemiDefMakes square matrices positive semi-definite.
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.
plotEFDRPlots an object of class 'EFDR'.
plot.optimizeParametersPlots an object of class 'optimizeParameters'.
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.
PeteHaitch/RUVcorr documentation built on May 8, 2019, 1:31 a.m.