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 |