Calculate the pMM distance — getpMMMatrix • GeDi

Calculate the pMM distance of all combinations of genesets in a given data set of genesets.

getpMMMatrix(
  genesets,
  ppi,
  alpha = 1,
  progress = NULL,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

genesets: a list, A list of genesets where each genesets is represented by list of genes.
ppi: a data.frame, Protein-protein interaction (PPI) network data frame. The object is expected to have three columns, Gene1 and Gene2 which specify the gene names of the interacting proteins in no particular order (symmetric interaction) and a column combined_score which is a numerical value of the strength of the interaction.
alpha: numeric, Scaling factor for controlling the influence of the interaction score. Defaults to 1.
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 pMM distance rounded to 2 decimal places.

References

See https://doi.org/10.1186/s12864-019-5738-6 for details on the original implementation.

Examples

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

ppi <- data.frame(
  Gene1 = c("PDHB", "VARS2"),
  Gene2 = c("IARS2", "PDHA1"),
  combined_score = c(0.5, 0.2)
)

pMM <- getpMMMatrix(genesets, ppi)

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

pMM <- getpMMMatrix(genes, ppi)