Abstract
In this chapter, the in silico systems genetics dataset, used as a benchmark in the rest of the book, is described in detail, in particular regarding its simulation by SysGenSIM. Morever, the algorithms underlying the generation of the gene expression data and the genotype values are fully illustrated.
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Notes
- 1.
SysGenSIM 1.0.2, version released on May \(8\mathrm{{th}}\), 2012. More information is available in the online manual at http://sysgensim.sourceforge.net.
- 2.
The average number of both ingoing and outgoing edges for a node: \(K = K_{\text {in}} + K_{\text {out}}\).
- 3.
Respectively, all the nodes from which the LSCC is reachable and that are not reachable from the LSCC, and all the nodes reachable from the LSCC but from which the LSCC cannot be reached.
- 4.
Nodes from which the LSCC cannot be reached, and that cannot be reached from the LSCC itself.
- 5.
Nodes connecting the in- to the out-component, and not belonging to the LSCC.
- 6.
In-degree and out-degree refer to the number of ingoing and outgoing edges of a node in a graph, respectively.
- 7.
The probability density function of an exponential distribution is \(f(x;\lambda ) = \lambda e^{-\lambda x}\) for \(x \ge 0\).
- 8.
The power law distribution is described by the probability density function \(f(x; \gamma ) = x^{-\gamma }\!\), for \(x \ge 0\).
- 9.
The condition is requested in the continuation of the algorithm.
- 10.
According to Haldane: \(r = 0.5 (1 - e^{-0.02 d})\).
- 11.
For recombinant inbred lines generated by selfing inbred line cross: \(p = 1 / ( 1 + 2 r)\).
References
Pinna A, Soranzo N, Hoeschele I, de la Fuente A (2011) Simulating systems genetics data with SysGenSIM. Bioinforma 27(17):2459–2462
Haldane JBS (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. J Genet 8:299–309
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugenics 12:172–175
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Pinna, A., Soranzo, N., Fuente, A., Hoeschele, I. (2013). Simulation of the Benchmark Datasets. In: de la Fuente, A. (eds) Gene Network Inference. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45161-4_1
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DOI: https://doi.org/10.1007/978-3-642-45161-4_1
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