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... |
ECDFPlot | Plot empirical cumulative distribution function for... |
eigenvaluePlot | Plot eigenvalues of SVD of the negtaive controls. |
empNegativeControls | Empirically choose negative control genes. |
findIQR | Find the inter quantile range. |
findMinmaxSamples | Find minimum and maximum samples in gene expression data. |
findWeights | Finds weights of each level of a factor. |
funcPara | Function to optimize parameters in parallel. |
funcThresh | Function to calculate correlation threshold in parallel. |
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. |
makePosSemiDef | Makes square matrices positive semi-definite. |
makeRankedList | Make ranked list of correlations. |
mashUp | Joining two correlation matrices by diagonal. |
optimizeParameters | Optimize parameters of removal of unwanted variation. |
PCAPlot | Plot principle component analysis for gene expression data. |
plotDesign | Plot nested design structure. |
plot.optimizeParameters | Plots an object of class 'optimizeParameters'. |
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. |
simulateGEdata | Simulate gene expression data. |
splitByFactor | Splitting a data set by a particular factor. |
wcor | Calculate weighted correlations. |
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