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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RUVcorr")
AuthorSaskia Freytag
Bioconductor views GeneExpression Normalization
Date of publicationNone
MaintainerSaskia Freytag <freytag.s@wehi.edu.au>
LicenseGPL-2
Version1.8.0

View on Bioconductor

Man 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...

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.

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.

Functions

assessQuality Man page
background Man page
calculateThreshold Man page
compareRanks Man page
correlationPlot Man page
ECDFPlot Man page
eigenvaluePlot Man page
empNegativeControls Man page
empNegativeControls.default Man page
empNegativeControls.simulateGEdata Man page
findIQR Man page
findMinmaxSamples Man page
findWeights Man page
funcPara Man page
funcThresh Man page
genePlot Man page
histogramPlot Man page
is.optimizeParameters Man page
is.simulateGEdata Man page
makePosSemiDef Man page
makeRankedList Man page
mashUp Man page
optimizeParameters Man page
PCAPlot Man page
plotDesign Man page
plot.optimizeParameters Man page
plotThreshold Man page
print.simulateGEdata Man page
prioritise Man page
RLEPlot Man page
RUVcorr Man page
RUVcorr-package Man page
RUVNaiveRidge Man page
RUVNaiveRidge.default Man page
RUVNaiveRidge.simulateGEdata Man page
simulateGEdata Man page
splitByFactor Man page
wcor Man page

Files

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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