You can also directly specify the mapping between genotypes andįitness and, thus, you can simulate on fitness landscapes of Interactions (and with fitness effects coming from any distribution you In addition, arbitrary numbers of genes without Modules, then, play the role of a “union operation” over the set Modules is the empty set) that performs a specific biologicalįunction. Modules, where each module is a set of genes (and the intersection between ( 2011): the restrictionsĮncoded in, say, CBNs or OT can be considered to apply not to genes, but to
This idea isĭiscussed in, for example, Raphael and Vandin ( 2015) and Gerstung et al. The above interactions in terms of modules, not genes. More generally, OncoSimulR now also allows you to specify arbitraryĮpistatic interactions between arbitrary collections of genes and to model,įor example, synthetic mortality or synthetic viability (again, involving anĪrbitrary number of genes, some of which might also depend on other genes, Mutations “A” and “B” differs depending on whether “A” appeared before orĪfter “B” (the actual case involves genes JAK2 and TET2). Paper by Ortmann and collaborators (Ortmann et al. With order effects, described in a recent cancer This is very different from “restrictions in the order ofĪccumulation of mutations”. Which mutations appear can also be incorporated, involving arbitrary numbers Moreover, different fitness effects related to the order in ( 2014) or the “semimonotone” model ofįarahani and Lagergren ( 2013). Other types of restrictions in the accumulation of genes, such as the XOR Since then, OncoSimulR has been vastly extended to allow you to specify Possibility of adding passenger mutations to the simulations and allowing (CBN: Beerenwinkel, Eriksson, and Sturmfels 2007 Gerstung et al. 1999 Szabo and Boucher 2008) or Conjunctive Bayesian Networks Mutations as specified, for example, by Oncogenetic Trees OncoSimulR was originally developed to simulate tumor progression withĮmphasis on allowing users to set restrictions in the accumulation of Its design emphasizes flexible specification of fitness and Reproducing populations without spatial structure (perfect Simulator for biallelic markers (wildtype vs. mutated) in asexually OncoSimulR is an individual- or clone-based forward-time genetic
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