GOKEGGSimsFromFile: GO- and KEGG- based Similarities Between two Genes

In ppiPre: Predict Protein-Protein Interactions Based on Functional and Topological Similarities

Description

Given an input file, this function will calculate KEGG-based similarity and three GO-based similarities between each protein pair in the file

Usage

GOKEGGSimsFromFile(input, output = "GOKEGGSims-ppiPre.csv", header = TRUE, sep = ",", 
                   organism = "yeast", drop = "IEA")

Arguments

input	CSV format PPI network, each line of which is two interacting proteins.
output	Result will be saved in output file.
header	If the input file contains header.
sep	The separator of the input file.
organism	One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "ecolik12", "ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat", "rhesus", "worm", "xenopus", "yeast" and "zebrafish."
drop	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.

Author(s)

Yue Deng <[e-mail]>

References

[1] S. Benabderrahmane, M. Smail-Tabbone, O. Poch, A. Napoli, and M.-D. Devignes, "IntelliGO: a new vector-based semantic similarity measure including annotation origin", BMC Bioinformatics, vol. 11, no. 1, p. 588, 2010.

[2] J. Z. Wang, Z. Du, R. Payattakool, P. S. Yu, and C.-F. Chen, "A new method to measure the semantic similarity of GO terms", Bioinformatics, vol. 23, no. 10, pp. 1274-1281, May. 2007.

[3] S. Jain and G. Bader, "An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology", BMC Bioinformatics, vol. 11, no. 1, p. 562, 2010.

[4] G. Yu, F. Li, Y. Qin, X. Bo, Y. Wu, and S. Wang, "GOSemSim: an R package for measuring semantic similarity among GO terms and gene products", Bioinformatics, vol. 26, no. 7, pp. 976-978, Apr. 2010.

See Also

TCSSGeneSim IntelliGOGeneSim GOKEGGSims

Examples

  #edges <- data.frame(node1=c("1132", "1133", "1134", "1134", "1145", "1147"),
  #                    node2=c("1134", "1134", "1145", "1147", "1147", "1149"))
  #graph<-igraph::graph.data.frame(edges,directed=FALSE)
  #samplefile <- "ppiPre-GOKEGGSimsFromFile-sample.csv"
  #write.csv(edges,file=samplefile,row.names=FALSE) 
  #GOKEGGSimsFromFile(input=samplefile,output="GOKEGGSims-ppiPre.csv", header=TRUE, sep=",",
  #                   organism="human") 
  #result<-read.csv(file="GOKEGGSims-ppiPre.csv")
  #print(result)

ppiPre documentation built on May 30, 2017, 4:33 a.m.