adjacency_matrix_from_data_frame {PrInCE} | R Documentation |
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.
adjacency_matrix_from_data_frame(dat, symmetric = TRUE, node_columns = c(1, 2))
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 ( |
an adjacency matrix between all interacting proteins
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)