Get Matrix of Meet-Min distances — getMeetMinMatrix • GeDi

Calculate the Meet-Min distance of all combinations of genesets in a given data set of genesets.

getMeetMinMatrix(
  genesets,
  progress = NULL,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

genesets: a list, A list of genesets where each genesets is represented by list of genes.
progress: a shiny::Progress() object, Optional progress bar object to track the progress of the function (e.g. in a Shiny app).
BPPARAM: A BiocParallel bpparam object specifying how parallelization should be handled. Defaults to BiocParallel::SerialParam()

Value

A Matrix::Matrix() with Meet-Min distance rounded to 2 decimal places.

Examples

## Mock example showing how the data should look like
genesets <- list(list("PDHB", "VARS2"), list("IARS2", "PDHA1"))
m <- getMeetMinMatrix(genesets)

## Example using the data available in the package
data(macrophage_topGO_example_small,
     package = "GeDi",
     envir = environment())
genes <- GeDi::getGenes(macrophage_topGO_example_small)
mm <- getMeetMinMatrix(genes)