Function reference • GeDi

All functions
`GeDi()`	GeDi main function
`buildClusterGraph()`	Build a cluster graph
`buildGraph()`	Construct a graph
`buildHistogramData()`	Prepare data for `gsHistogram()`.
`calculateJaccard()`	Calculate the Jaccard distance
`calculateKappa()`	Calculate the Kappa distance
`calculateSorensenDice()`	Calculate the Sorensen-Dice distance
`checkInclusion()`	Check for subset inclusion
`clustering()`	Cluster genesets.
`distanceDendro()`	Plot a dendrogram
`distanceHeatmap()`	Plot a heatmap
`.checkGenesets()`	Check genesets format
`.checkPPI()`	Check PPI format
`.checkScores()`	Check distance scores format
`.filterGenesets()`	Filter Genesets from the input data
`.findSeparator()`	Make an educated guess on the separator character
`.getClusterDatatable()`	Map each geneset to the cluster it belongs
`.getGenesetDescriptions()`	Title
`.getNumberCores()`	Determine the number of cores to use for a function
`.graphMetricsGenesetsDT()`	Generate a `data.frame` of graph metrics
`.sepguesser()`	Make an educated guess on the separator character
`enrichmentWordcloud()`	Visualize the results of an enrichment analysis as word cloud
`fuzzyClustering()`	Find cluster from initial seeds
`getAdjacencyMatrix()`	Construct an adjacency matrix
`getAnnotation()`	Get the annotation of a STRINGdb object
`getBipartiteGraph()`	Construct a bipartite graph
`getClusterAdjacencyMatrix()`	Construct an adjacency matrix
`getGenes()`	Split string of genes
`getGraphTitle()`	Build up the node title
`getId()`	Get NCBI ID
`getInteractionScore()`	Calculate interaction score for two genesets
`getJaccardMatrix()`	Get Matrix of Jaccard distances
`getKappaMatrix()`	Get Matrix of Kappa distances
`getMeetMinMatrix()`	Get Matrix of Meet-Min distances
`getPPI()`	Download Protein-Protein Interaction (PPI)
`getSorensenDiceMatrix()`	Get Matrix of Sorensen-Dice distances
`getStringDB()`	Get the STRING db entry of a species
`getpMMMatrix()`	Calculate the pMM distance
`goSimilarity()`	Calculate similarity of GO terms
`gsHistogram()`	Create a histogram plot for gene set sizes
`kNN_clustering()`	Calculate clusters based on kNN clustering
`macrophage_KEGG_example`	A sample input RData file
`macrophage_Reactome_example`	A sample input RData file
`macrophage_topGO_example`	A sample input RData file
`macrophage_topGO_example_small`	A small sample input RData file
`pMMlocal()`	Calculate local pMM distance
`ppi_macrophage_topGO_example_small`	PPI
`sample_geneset`	A sample input text file
`sample_geneset_broken`	A broken input text file
`sample_geneset_empty`	An empty input text file
`sample_geneset_small`	A small sample input text file
`scaleGO()`	Scaling (distance) scores
`scores_macrophage_topGO_example_small`	Sample scores
`seedFinding()`	Find clustering seeds

Reference

All functions