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

## Documentation for package ‘RUVcorr’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

RUVcorr-package | Removal of unwanted variation for gene-gene correlations.
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.
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.