get_adj_matrix {net4pg} | R Documentation |
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 |
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)
[Package net4pg version 0.1.1 Index]