readNet: Fetching true network from .sif file

In netmes: Exploratory Analysis of Gene Networks with Netmes, An R package for network-based measures

Description

This function takes the sythetic .sif file, which has interactions of genes, as input and converts it into an adjanceny matrix.

Usage

readNet(infile, infilepath)

Arguments

infile	The path for the .sif file that has true interactions of the genes.
infilepath	The path of the directory, where all the data files kept.

Details

It assigns 1 for 'ac' and and -1 for 're' and then fills by zeros for the rest of the matrix. This function is for synthetic networks as the gene names are expilicit as numbered. Note that the matrix is not symmetric. An example of .sif file can be obtained from SynTRen where the underlying network has gene labels as 'numbers'.

Value

readNet returns the genes' relation matrix where activator edges, repressor edges and absence of edges are represented by 1, -1 and 0 respectively.

References

Gokmen Altay and Frank Emmert-Streib. Revealing differences in gene network inference algorithms on the network level by ensemble methods. Bioinformatics, 2010, 26(14),1738-1744.

Frank Emmert-Streib, Gokmen Altay. Local network-based measures to assess the inferability of different regulatory networks. IET Syst. Biol. 2010, Volume 4, Issue 4, p.277-288.

Examples

# infile <- "./netmes/data/networkDAG.sif"
# infilepath <- "./netmes/data/syn/"

# net <- readNet(infile, infilepath)   
# tnet <- abs(net) + abs(t(net)) # true network (make symmetric)
# tnet <- 1*(tnet > 0)           # in case there were bi-directional connections

netmes documentation built on May 2, 2019, 5:21 p.m.