Description Usage Arguments Author(s) References See Also Examples
View source: R/TopologicSims.r
Given an PPI network, this function will calculate three topological similarities of each protein pair in the network.
1 2 | TopologicSims(inputfile, outputfile = "TopologicSims-ppiPre.csv", header = TRUE,
sep = ",")
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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. |
Yue Deng <anfdeng@163.com>
[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.
1 2 3 4 5 6 7 8 | 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)
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