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

[Up] [Top]

Documentation for package ‘RUVcorr’ version 1.36.0

Help 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 correlations.
ECDFPlot Plot empirical cumulative distribution function for correlations.
eigenvaluePlot Plot eigenvalues of SVD of the negtaive controls.
empNegativeControls Empirically choose negative control genes.
empNegativeControls.default Empirically choose negative control genes.
empNegativeControls.simulateGEdata Empirically choose negative control genes.
findWeights Finds weights of each level of a factor.
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.
is.Threshold Checking 'Threshold' class.
is.Weights Checking 'Weights' class.
optimizeParameters Optimize parameters of removal of unwanted variation.
PCAPlot Plot principle component analysis for gene expression data.
plot.optimizeParameters Plots an object of class 'optimizeParameters'.
plotDesign Plot nested design structure.
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.
RUVNaiveRidge.default Removal of unwanted variation for gene correlations.
RUVNaiveRidge.simulateGEdata Removal of unwanted variation for gene correlations.
simulateGEdata Simulate gene expression data.
wcor Calculate weighted correlations.