Co-expression Graph Analyzer


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Documentation for package ‘coga’ version 0.01-1

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coga-package The coga Package
absMaxMean AbsMaxMean method for collapsing probe sets to genes
absMinMean AbsMinMean method for collapsing probe sets to genes
adjacencyMatrix 'adjacencyMatrix' creates a function that infers a graph from gene expression data.
average Average method for collapsing probe sets to genes
averageBetweennessCentrality Average betweenness centrality
averageClosenessCentrality Average closeness centrality
averageClusteringCoefficient Average clustering coefficient
averageDegreeCentrality Average degree centrality
averageEigenvectorCentrality Average eigenvector centrality
averageShortestPath Average shortest path
betweennessCentrality Betweenness centrality
betweennessCentralityTest Betweenness centrality test
closenessCentrality Closeness centrality
closenessCentralityTest Closeness centrality test
clusteringCoefficient Clustering coefficient
clusteringCoefficientTest Clustering coefficient test
collapseExprData Collapse probe sets to gene symbols
degreeCentrality Degree centrality
degreeCentralityTest Degree centrality test
degreeDensities Density functions of the degrees of two graphs
degreeDistributionTest Degree distribution test
diffNetAnalysis CoGA differential network analysis
eigenvectorCentrality Eigenvector centrality
eigenvectorCentralityTest Eigenvector centrality test
JSdegree Jensen-Shannon divergence between the density functions of the degrees of two graphs
labelsAux Label
maxMean MaxMean method for collapsing probe sets to genes
maxRowVariance MaxRowVariance method for collapsing probe sets to genes Choose the row with the highest variance
me Me method for collapsing probe sets to genes
minMean MinMean method for collapsing probe sets to genes
readChipFile Read annotation data (*.chip)
readClsFile Read categorical class file (*.cls)
readExprTxtFile Read gene expression data (*.txt)
readGmtFile Read a collection of gene sets (*.gmt)
runCoga Run CoGA
shortestPathTest Shortest path test
spectralDistributionTest Spectral distribution test
spectralEntropies Spectral entropies
spectralEntropyTest Spectral entropy test