| read.OCG {linkcomm} | R Documentation |
Read an OCG Partition File into R
Description
This function reads in an OCG partition file and converts it into an OCG object for use in R.
Usage
read.OCG(file, elfile = NULL, verbose = FALSE, keep.out = FALSE)
Arguments
file |
A character string naming the OCG partition file. |
elfile |
A character string naming the file containing the network that the OCG partition is based upon. |
verbose |
Logical, whether to print progress to the screen. Defaults to FALSE. |
keep.out |
Logical, whether to keep the intermediate files written when reading in the OCG partition. Defaults to FALSE. |
Value
An object of class OCG, which is a list containing the following elements:
numbers |
An integer vector with the number of edges, nodes, and communities. |
modularity |
An integer number specifying the modularity of the network. |
Q |
A real number specifying the value of Q generated by the OCG algorithm. |
nodeclusters |
A data frame consisting of 2 columns; the first contains node names, and the second contains single community IDs for each node. All communities and their nodes are represented, but not necessarily all nodes. |
numclusters |
A named integer vector. Names are node names and integer values are the number of communities to which each node belongs. |
igraph |
An object of class |
edgelist |
A character matrix with 2 columns containing the nodes that interact with each other. |
clustsizes |
A named integer vector. Names are community IDs and integer values indicate the number of nodes that belong in each community. |
Author(s)
Alex T. Kalinka alex.t.kalinka@gmail.com
References
Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.
Examples
## Read an OCG partition file into R.
## Not run: oc <- read.OCG(file = "OCG_partition.txt", elfile = "network.txt")