plotDs: TPR for all of the re or ac types of edges

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

Description

This function takes the object that is the result of TPRall function and Sm and computes Ds values and plot it.

Usage

plotDs(TPReALL, Sm, fig=TRUE)

Arguments

TPReALL	Object that is the result of TPRall function.
Sm	Sum of degrees of nodes.
fig	By default it saves the figures of the results. If not wanted then set it FALSE.

Details

The influence of the degree of nodes on the inferability of edges is computed and plotted as Ds.eps.

Value

plotDs returns an object of class '"ds"' which is a list with components:

gem	Mean values of the degree of nodes.
ges	Standard deviation values of the degree of nodes.
Ds.eps	(If fig is set as TRUE or by default) Saves the figure Ds.eps to the current directory where x-axis sum of degree values, Ds, and y-axis is for corresponding TPR values.

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.)

# Sm <- sumdeg(net)

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

# TPRs <- TPRall(res)  #also save the fig

# Ds <-plotDs(TPRs$TPReALL, Sm)

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