read.OCG function

Read an OCG Partition File into R

This function reads in an OCG partition file and converts it into an OCG object for use in R.

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.

Returns

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 igraph. The network is represented here as an igraph object.

• 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.

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.

Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

Examples

## Read an OCG partition file into R.
## Not run: oc <- read.OCG(file = "OCG_partition.txt", elfile = "network.txt")