Find cluster from initial seeds — fuzzyClustering • GeDi

Merge the initially determined seeds to clusters.

fuzzyClustering(seeds, threshold)

Arguments

seeds: A list of seeds, e.g. determined by GeDi::seedFinding() function
threshold: numerical, A threshold for merging seeds

Value

A list of clusters

References

See https://david.ncifcrf.gov/helps/functional_classification.html#clustering for details on the original implementation

Examples

## Mock example showing how the data should look like

seeds <- list(c(1:5), c(6:10))
cluster <- fuzzyClustering(seeds, 0.5)

## Example using the data available in the package
data(scores_macrophage_topGO_example_small,
     package = "GeDi",
     envir = environment())

seeds <- seedFinding(scores_macrophage_topGO_example_small,
                     simThreshold = 0.3,
                     memThreshold = 0.5)
cluster <- fuzzyClustering(seeds, threshold = 0.5)