adjacency_matrix_from_data_frame {PrInCE} | R Documentation

## Create an adjacency matrix from a data frame

### 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)

[Package PrInCE version 1.0.1 Index]