Description Usage Arguments Value Author(s) References Examples
Identifying miRNA sponge modules from network. Possible methods include FN, MCL, LINKCOMM and MCODE.
1 |
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. |
A list of miRNA sponge modules.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
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.
1 2 3 4 5 | # Obtain miRNA-target interaction data file "miR2Target.csv" in csv format
miR2Target <- system.file("extdata", "miR2Target.csv", package="miRsponge")
miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
spongenetwork_Cluster <- netModule(miRHomologyceRInt[, 1:2])
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