A sparse adjacency matrix representing a protein-protein interaction network compiled from multiple databases.
Format
A dgCMatrix object from the
Matrix package, where a value of 1 indicates
a connection (interaction) between two genes, and 0 indicates no
connection. The rows and columns of the matrix correspond to gene
identifiers, and the matrix is square and symmetric, representing an
undirected adjacency network.
Source
The protein-protein interaction data was compiled from the following databases:
KEGG (https://www.genome.jp/kegg/)
Reactome (https://reactome.org/)
Biocarta (https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways)
NCI (https://cancer.gov/about-nci)
SPIKE (https://www.cbrc.kaust.edu.sa/spike/)
HumanCyc (https://humancyc.org/)
Panther (http://www.pantherdb.org/)
Details
The `ppi` data set is a sparse adjacency matrix representing a protein-protein interaction network. The network was compiled from seven databases: KEGG, Reactome, Biocarta, NCI, SPIKE, HumanCyc, and Panther.
The rows and columns of the matrix correspond to gene identifiers, and the order of the genes is consistent across rows and columns. The matrix is square and symmetric, representing an undirected network, where an interaction between gene A and gene B is represented by a 1 in both the (A, B) and (B, A) positions of the matrix.
Examples
library(Matrix)
data(ppi, package = "labyrinth")
# Access a specific element of the matrix
dim(ppi)
#> [1] 12836 12836
ppi[1, 2] # Interaction between gene 1 and gene 2
#> [1] 0
# Convert to a dense matrix for visualization or analysis
dense_ppi <- as.matrix(ppi)
#> Warning: sparse->dense coercion: allocating vector of size 1.2 GiB