to_adjacency_matrix: Create an adjacency matrix from a pairwise data frame

In fosterlab/CFTK: The Co-Fractionation Toolkit

Description

Convert a data frame containing pairwise interactions into an adjacency matrix. The resulting square adjacency matrix contains ones for interacting proteins and zeroes for non-interacting proteins.

Usage

to_adjacency_matrix(dat, symmetric = TRUE, node_columns = c(1, 2))

Arguments

dat	a data frame containing pairwise interactions
symmetric	if true, interactions in both directions will be added to the adjacency matrix
node_columns	a vector of length two, denoting either the indices (integer vector) or column names (character vector) of the columns within the data frame containing the nodes participating in pairwise interactions; defaults to the first two columns of the data frame (c(1, 2))

Value

an adjacency matrix between all interacting proteins

Examples

ppi = data.frame(protein_A = paste0("protein", seq_len(10)),
                 protein_B = paste0("protein", c(rep(3, 2), rep(5, 5), 
                                    rep(7, 3))), stringsAsFactors = FALSE)
adj = to_adjacency_matrix(ppi)

fosterlab/CFTK documentation built on Jan. 19, 2021, 10:31 p.m.