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. |