# Defining and visualizing the distances between different genesets

## Documentation for package ‘GeDi’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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
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
enrichmentWordcloud | Visualize the results of an enrichment analysis as word cloud
fuzzyClustering | Find cluster from initial seeds
GeDi | GeDi main function
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
getpMMMatrix | Calculate the pMM distance
getPPI | Download Protein-Protein Interaction (PPI)
getSorensenDiceMatrix | Get Matrix of Sorensen-Dice distances
getStringDB | Get the STRING db entry of a species
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