readSifNet: Fetching true biological network from .sif file

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

Description

This function is for biological networks where the names of the genes are arbitrary and needs to be derived along with the interaction of the genes. It provides the adjanceny matrix and and the corresponding gene names of the matrix.

Usage

readSifNet(infilenet, infilepath)

Arguments

infilenet	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 the rest of the matrix. Note that the matrix is not symmetric.

Value

readSifNet returns an object of class '"res"' which is a list with components:

net	the genes' relation matrix where activator edges, repressor edges and absence of edges are represented by 1, -1 and 0 respectively.
names	the gene names corresponding to the row and column names of the adjanceny matrix.

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.

See Also

readSifNet, evalnetworks, evalnetworksNames

Examples

# infilenet <- "./netmes/data/networkEcoli.sif"
# infilepath <- "./netmes/data/bio/"

# resEC <- readSifNet(infilenet, infilepath) # true network (+1 edge/ activator - -1 edges/repr.
# net <- resEC$net
# tnet <- abs(resEC$net) + abs(t(resEC$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.