simulatedData: Random Generation Networks for RNA-Seq Data

In synRNASeqNet: Synthetic RNA-Seq Network Generation and Mutual Information Estimates

Description

A function that use a stochastic BA-modelfor building a graph and the simulated RNA-Seq counts (from a Poisson (multivariate or over-dispersed) distribution) that encode the underlying graph structure.

Usage

simulatedData(p = 50, n = 100, mu = 100, sigma = 0.25, ppower = 1,
              noise = F, seed = NULL)

Arguments

p	the number of genes in the networks.
n	the number of simulated samples for each gene.
mu	the average mean of the simulated Poisson distributions.
sigma	the over-dispersed sd value in the case of over-dispersed Poisson simulation.
ppower	the power of the preferential attachment for the BA-model.
noise	logical. Should same noise be added to the data or not?
seed	a single value, interpreted as an integer, in order to control the simulated data.

Value

graph	the graph generated with the BA-model.
adjMat	the related adjacency matrix that encodes the underlying graph structure.
counts	the simulated RNA-Seq counts matrix.

Author(s)

Luciano Garofano [e-mail], Stefano Maria Pagnotta, Michele Ceccarelli

References

Barabasi A.L., Albert R. (1999). Emergence of scaling in random networks. Science, 286 509-512.

Gallopin M., Rau A., Jaffrezic F. (2013). A Hierarchical Poisson Log-Normal Model for Network Inference from RNA Sequencing Data. PLOSone.

See Also

mainNetFunction

Examples

simData <- simulatedData(p = 50, n = 100, mu = 100, sigma = 0.25,
                        ppower = 0.73, noise = FALSE)
plot(simData$graph)

counts <- simData$counts
adjMat <- simData$adjMat

Example output

Loading required package: parallel
Loading required package: parmigene
Loading required package: GenKern
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

synRNASeqNet documentation built on May 2, 2019, 6:01 a.m.