ppiPre (version 1.9)

TopologicSims: Compute topological similarities from user input file

Description

Given an PPI network, this function will calculate three topological similarities of each protein pair in the network.

Usage

TopologicSims(inputfile, outputfile = "TopologicSims-ppiPre.csv", header = TRUE,  sep = ",")

Arguments

inputfile

CSV format PPI network, each line of which is an two interacting proteins.

outputfile

Result will be saved in output file.

header

If the input file contains header.

sep

The separator of the input file.

References

[1] T. Zhou, L. Lv, and Y.-C. Zhang, "Predicting missing links via local information", The European Physical Journal B - Condensed Matter and Complex Systems, vol. 71, no. 4, pp. 623-630, Oct. 2009

[2] L. A. Adamic and E. Adar, "Friends and neighbors on the Web", Social Networks, vol. 25, no. 3, pp. 211-230, 2003.

[3] P. Jaccard, "?tude comparative de la distribution florale dans une portion des Alpes et des Jura", Bull. Soc. Vaud. Sci. Nat, vol. 37, p. 541, 1901.

See Also

AASim JaccardSim RASim

Examples

  edges <- data.frame(node1=c("1132", "1133", "1134", "1134", "1145", "1147", "1147", "1147"),
                      node2=c("1134", "1134", "1145", "1147", "1147", "1148", "1149", "1150"))
  graph<-igraph::graph.data.frame(edges,directed=FALSE)
  samplefile <- "ppiPre-TopologicSims-sample.csv"
  write.csv(edges,file=samplefile,row.names=FALSE) 
  TopologicSims(samplefile,outputfile="TopologicSimstest-ppiPre.csv", header=TRUE, sep=",") 
  result<-read.csv(file="TopologicSimstest-ppiPre.csv")
  print(result)