get_adj_matrix: Generate adjacency matrix

In laurafancello/net4pg: Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Generate adjacency matrix

Description

Generate an adjacency matrix representing protein-to-protein connections, based on shared peptides. It is generated by cross product of the incidence matrix of peptide-to-protein mappings.

Usage

get_adj_matrix(incM)

Arguments

incM	a logical matrix containing the incidence matrix with its column and row names (respectively, protein and peptide identifiers) names and 0 or 1 values indicating whether or not the peptide maps on the corresponding protein.

Value

a numeric matrix containing the adjacency matrix, with value >0 or 0 indicating whether or not two proteins are identified by shared peptide(s)

Author(s)

Laura Fancello

Examples

# Read the tab-delimited file containing he proteome incidence matrix
incM_filename <- system.file( "extdata"
                             , "incM_example"
                             , package = "net4pg"
                             , mustWork = TRUE)
rownames_filename <- system.file( "extdata"
                                  , "peptideIDs_incM_example"
                                  , package = "net4pg"
                                  , mustWork = TRUE)
colnames_filename <- system.file( "extdata"
                                 , "proteinIDs_incM_example"
                                 , package = "net4pg"
                                 , mustWork = TRUE)
incM <- read_inc_matrix(incM_filename=incM_filename
                 , colnames_filename=colnames_filename
                 , rownames_filename=rownames_filename)
# Only retain proteins with at least one shared peptide and all peptides
# mapping on such proteins.
incM_reduced <- reduce_inc_matrix(incM)
# Generate adjacency matrix describing protein-to-protein mappings
adjM <- get_adj_matrix(incM_reduced)

laurafancello/net4pg documentation built on July 1, 2022, 1:34 p.m.