Find V motifs in protein-protein interactions
Usage
find_ppi_v(edgelist = NULL, paralogs = NULL, count_only = FALSE)
Arguments
- edgelist
A 2-column data frame with protein 1 in column 1 and
protein 2 in column 2.
- paralogs
A 2-column data frame with gene IDs for each paralog
in the paralog pair.
- count_only
Logical indicating whether the function should return
only motif counts as a numeric scalar. If FALSE, it will return
a character vector of motifs. Default: FALSE.
Value
A character vector with V motifs represented
in the format paralog1-partner-paralog2.
Details
This function aims to find the number of paralogous gene
pairs that share an interaction partner.
Examples
data(gma_ppi)
data(gma_paralogs)
edgelist <- gma_ppi
paralogs <- gma_paralogs[gma_paralogs$type == "WGD", 1:2]
motifs <- find_ppi_v(edgelist, paralogs)
