netModule: Identifying miRNA sponge modules from network

In miRspongeR: Identification and analysis of miRNA sponge interaction networks and modules

Description

Identifying miRNA sponge modules from network. Possible methods include FN, MCL, LINKCOMM and MCODE.

Usage

netModule(spongenetwork, method = "MCL", directed = FALSE, modulesize = 3, save = FALSE)

Arguments

spongenetwork	Input miRNA sponge interaction network.
method	Cluster method, can select one of FN, MCL, LINKCOMM and MCODE.
directed	A logical value, the network is directed or not.
modulesize	The size cutoff of the identified modules.
save	A logical value, save the identified modules or not.

Value

A list of miRNA sponge modules.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

1. Clauset A, Newman ME, Moore C. Finding community structure in very large networks. Phys Rev E Stat Nonlin Soft Matter Phys., 2004, 70(6 Pt 2):066111.

2. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 2002, 30(7):1575-84.

3. Kalinka AT, Tomancak P. linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics, 2011, 27(14):2011-2.

4. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 2003, 4:2.

Examples

# Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
spongenetwork_Cluster <- netModule(miRHomologyceRInt[, 1:2])

miRspongeR documentation built on Nov. 19, 2020, 2:01 a.m.