adjacency_matrix_from_data_frame: Create an adjacency matrix from a data frame

In fosterlab/PrInCE-R: Predicting Interactomes from Co-Elution

Description

Convert a data frame containing pairwise interactions into an adjacency matrix. The resulting square adjacency matrix contains ones for proteins that are found in interactions and zeroes otherwise.

Usage

adjacency_matrix_from_data_frame(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))))
adj <- adjacency_matrix_from_data_frame(ppi)

fosterlab/PrInCE-R documentation built on Dec. 11, 2020, 3:51 p.m.