motifcount3: Motif statistics for regulatory networks

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

Description

This function takes the adjacency matrix, averaged mutual information matrix for the inferred edges, averaged mutual information matrix and number of genes as input. It returns

the data sets folder path and number of mutual information steps for the therhold mutual information. Considering 3 gene case, it computes number of motifs, probability to observe a motif, average mutual information of motifs and node indices for motifs.

Usage

motifcount3(net, rmat, MImat)

Arguments

net	adjacency matrix of genes (not symmetric).
rmat	averaged mutual information matrix for the inferred edges of the overall experiments.
MImat	averaged mutual information matrix of the overall experiments.

Details

It only consider 3 genes case and search for all the possible motifs with 3 genes.

Value

motifcount3 returns an object of class '"res"' which is a list with components:

moty	number of motifs.
motyprob	probability to observe a motif.
motyMI	average mutual information of motifs.
emotnodes	node indices for motifs.

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

plotMotifs, evalnetworks, evalnetworksNames

Examples

# E <- 5 # number of experiments (data sets)

# infile <- "./netmes/data/networkDAG.sif"
# infilepath <- "./netmes/data/syn/"
#This is an example path. Change this path wrt the path of data in your computer.

# net <- readNet(infile, infilepath) # true network (+1 edge/ activator - -1 edges/repr.)

# res <- evalnetworks(E, net, infilepath)

# res2 <- motifcount3(net, res$rmat, res$aveMImat)

# plotMotifs(res2)

# if True Reconstruction Rate wished to be plotted
# envm <- res2$motyprob
# y <- c()
# xg <- c()
# i <- 2
# aux <- get(as.character(i), envir = envm)
# y <- append(y, aux, after = length(y))
# xg <- append(xg, rep(1, length(aux)), after = length(xg))
# boxplot(y ~ xg, names = c("DAG"), ylab = expression(p), cex.lab = 1.7, cex.axis = 1.6, col = c("darkred") )

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