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RUVcorr (version 1.4.2)

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

Description

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

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Version

Version

1.4.2

License

GPL-2

Maintainer

Saskia Freytag

Last Published

February 15th, 2017

Functions in RUVcorr (1.4.2)

is.simulateGEdata

Checking simulateGEdata class.
plotThreshold

Plots an object of class Threshold.
PCAPlot

Plot principle component analysis for gene expression data.
RUVNaiveRidge

Removal of unwanted variation for gene correlations.
plot.optimizeParameters

Plots an object of class optimizeParameters.
optimizeParameters

Optimize parameters of removal of unwanted variation.
findIQR

Find the inter quantile range.
splitByFactor

Splitting a data set by a particular factor.
plotDesign

Plot nested design structure.
RLEPlot

Plots different versions of relative log expression plots
findWeights

Finds weights of each level of a factor.
eigenvaluePlot

Plot eigenvalues of SVD of the negtaive controls.
compareRanks

Compare ranking of known reference gene pairs.
makeRankedList

Make ranked list of correlations.
correlationPlot

Correlation plot to compare estimated correlations with true correlations.
empNegativeControls

Empirically choose negative control genes.
histogramPlot

Plot histogram of correlations.
genePlot

Plot of means and inter-quantile ranges of all genes.
calculateThreshold

Calculates the correlation threshold.
background

Randomly choose background genes.
is.optimizeParameters

Checking optimizeParameters class.
print.simulateGEdata

Print an object of class simualteGEdata.
assessQuality

Quality assessment for cleaning procedures.
funcThresh

Function to calculate correlation threshold in parallel.
RUVcorr

Removal of unwanted variation for gene-gene correlations.
mashUp

Joining two correlation matrices by diagonal.
ECDFPlot

Plot empirical cumulative distribution function for correlations.
prioritise

Prioritising candidate genes.
wcor

Calculate weighted correlations.
funcPara

Function to optimize parameters in parallel.
makePosSemiDef

Makes square matrices positive semi-definite.
findMinmaxSamples

Find minimum and maximum samples in gene expression data.
simulateGEdata

Simulate gene expression data.