HEMDAG (version 2.1.3)

weighted.adjacency.matrix: Weighted Adjacency Matrix

Description

Construct a Weighted Adjacency Matrix (wadj matrix) of a graph

Usage

weighted.adjacency.matrix(file = "edges.txt", compressed = TRUE,
  nodename = TRUE)

Arguments

file

name of the plain text file to be read (def. edges). The format of the file is a sequence of rows. Each row corresponds to an edge represented through a pair of vertices separated by blanks and the weight of the edges. For instance: nodeX nodeY score

compressed

boolean value:

• TRUE (def.): the input file must be in a .gz compressed format;

• FALSE: the input file must be in a plain text format;

nodename

boolean value:

• TRUE (def.): the names of nodes are gene symbol (i.e. characters);

• FALSE: the names of the nodes are entrez gene ID (i.e. integer numbers);

Value

a named symmetric weighted adjacency matrix of the graph

Details

The input paramenter nodename sorts the row names of the wadj matrix in increasing order if they are integer number or in alphabetic order if they are characters.

Examples

# NOT RUN {
edges <- system.file("extdata/edges.txt", package="HEMDAG");
W <- weighted.adjacency.matrix(file=edges, compressed=FALSE, nodename=TRUE);
# }