Calculate local pMM distance — pMMlocal • GeDi

Calculate the local pMM distance of two genesets.

pMMlocal(a, b, ppi, maxInteract, alpha = 1)

Arguments

a, b: character vector, set of gene identifiers.
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.
maxInteract: numeric, Maximum interaction value in the PPI.
alpha: numeric, Scaling factor for controlling the influence of the interaction score. Defaults to 1.

Value

The pMMlocal score between the two gene sets.

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
a <- c("PDHB", "VARS2")
b <- c("IARS2", "PDHA1")

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

pMM_score <- pMMlocal(a, b, ppi, maxInteract)

## 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())
maxInteract <- max(ppi_macrophage_topGO_example_small$combined_score)

pMMlocal <- pMMlocal(genes[1], genes[2], ppi, maxInteract)