FNPre: Predict false negative interactions based on topological...

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

Description

User can predict false negative interactions from an given PPI network, based on one to three topological similarities.

Usage

FNPre(file,indicator=c("RA","AA","Jaccard"),threshold=0.1, 
      output="FalseNegativePreResult-ppiPre.csv") 

Arguments

file	CSV format PPI network given by user, each line of which includes two interacting proteins.
indicator	Can be any combination of "RA", "AA", and "Jaccard", indicate the similarities used.
threshold	The ratio of false negative interactions to positive interactions in the network.
output	Result will be saved in the output file.

Author(s)

Yue Deng <[e-mail]>

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, "Etude 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"),node2=c("1134", "1134", "1145"))
  graph<-igraph::graph.data.frame(edges,directed=FALSE)
  samplefile <- "ppiPre-FNPre-sample.csv"
  write.csv(edges,file=samplefile,row.names=FALSE) 
  FNPre(file=samplefile, indicator = c("RA", "AA"), threshold = 0.1)
  result<-read.csv(file="FalseNegativePreResult-ppiPre.csv")
  print(result)

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