find_ppi_v: Find V motifs in protein-protein interactions

In almeidasilvaf/magrene: Motif Analysis In Gene Regulatory Networks

Find V motifs in protein-protein interactions

Description

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.

Details

This function aims to find the number of paralogous gene pairs that share an interaction partner.

Value

A character vector with V motifs represented in the format paralog1-partner-paralog2.

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)

almeidasilvaf/magrene documentation built on March 16, 2023, 4:29 a.m.