birewire.analysis.dsg: Analysis of Jaccard similarity trends across switching steps.

In BiRewire: High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Description

This function performs a sequence of max.iter.pos (and max.iter.pos) switching steps on the positive (and negative) part of the input dsg g and computes the Jaccard similarity between g (the initial network) and its rewired version each step switching steps. This procedure is pefromed n.networks times and a simple explorative plot, with mean and CI, is visualized if display is set to TRUE. The plot shows the trend of the Jaccad Index relative to the positve (and negative) part of g.

Usage

birewire.analysis.dsg(dsg, step=10, max.iter.pos='n',max.iter.neg='n',accuracy=0.00005,
			     verbose=TRUE,MAXITER_MUL=10,exact=FALSE,n.networks=50,display=TRUE)

Arguments

dsg	The initial dsg object (see birewire.induced.bipartite). Note that the dsg must contain a list of two incidence matrices and not igraph bipartite graphs.
step	10 (default): the interval (in terms of switching steps) at which the Jaccard index between g and the its current rewired version is computed;
max.iter.pos	"n" (default) the number of switching steps to be performed (or if exact==TRUE the number of successful switching steps) for the positive part of g. See birewire.rewire.bipartite for more details;
max.iter.neg	"n" (default) the same of max.iter.p but relative to the negative part;
accuracy	0.00005 (default) is the desired level of accuracy reflecting the average distance between the Jaccard index at the N-th step and its analytically derived fixed point in terms of fracion of common edges;
verbose	TRUE (default). When TRUE a progression bar is printed during computation;
MAXITER_MUL	10 (default). If exact==TRUE in order to prevent a possible infinite loop the program stops anyway after MAXITER_MUL*max.iter iterations;
exact	FALSE (default). If TRUE the program performs max.iter swithcing steps, otherwise the program will count also the not-performed swithcing steps;
n.networks	50 (default), the number of independent rewiring process starting from the same inital graph from which the mean value and the CI is computed.
display	TRUE (default). If TRUE two explorative plots are displayed summarizing the trend of the Jaccard index in terms of mean and confidence interval.

Details

This procedure acts in the same way of birewire.analysis.bipartite but in the case of dsg. The similarity is measurwe using birewire.similarity.dsg.

Value

A list containing two lists: data that is a list collecting all the Jacard index computed (each row is a run of the SA) for the positive and negative part, and a list with the analytically derived lower bounds N for the positive and negative part of g.

Author(s)

Andrea Gobbi
Maintainer: Andrea Gobbi <[e-mail]>

References

Iorio, F. and and Bernardo-Faura, M. and Gobbi, A. and Cokelaer, T.and Jurman, G.and Saez-Rodriguez, J. (2016) Efficient randomization of biologicalnetworks while preserving functionalcharacterization of individual nodes Bioinformatics 2016 1 (17):542 doi: 10.1186/s12859-016-1402-1.

Gobbi, A. and Iorio, F. and Dawson, K. J. and Wedge, D. C. and Tamborero, D. and Alexandrov, L. B. and Lopez-Bigas, N. and Garnett, M. J. and Jurman, G. and Saez-Rodriguez, J. (2014) Fast randomization of large genomic datasets while preserving alteration counts Bioinformatics 2014 30 (17): i617-i623 doi: 10.1093/bioinformatics/btu474.

Jaccard, P. (1901), Étude comparative de la distribution florale dans une portion des Alpes et des Jura, Bulletin de la Société Vaudoise des Sciences Naturelles 37: 547–579.

R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon (2003), On the uniform generation of random graphs with prescribed degree sequences, eprint arXiv:cond-mat/0312028

Examples

library(BiRewire)
data(test_dsg)
dsg <-  birewire.induced.bipartite(test_dsg,sparse=FALSE)

a=birewire.analysis.dsg(dsg,verbose=FALSE,step=1,exact=TRUE,max.iter.pos=200,max.iter.neg=50)

BiRewire documentation built on Nov. 8, 2020, 8:09 p.m.