get_cc {net4pg} | R Documentation |
Generate graph and calculate its connected components
Description
Build a graph of protein-to-protein connections from adjacency matrix and calculate its connected components.
Usage
get_cc(adjM)
Arguments
adjM |
a |
Value
a list
of two elements: i. a graph
representing
protein-to-protein connections encoded by the adjacency matrix; ii. a
list
of vectors
(one for each connected component) enumerating
protein members of each connected component.
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)
# Generate graph of protein-to-protein connections and calculate its
# connected components
multProteinCC <- get_cc(adjM)
[Package net4pg version 0.1.1 Index]