Network Reverse Engineering with Approximate Bayesian Computation

We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as scale-freeness and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-engineering consists in using gene expressions over time or over different experimental conditions to discover the structure of the gene network in a targeted cellular process. The fact that gene expression data are usually noisy, highly correlated, and have high dimensionality explains the need for specific statistical methods to reverse engineer the underlying network.


News

networkABC 0.5-2

  • Added citation for package

networkABC 0.5-1

  • Updated code to add R_forceSymbols(dll, TRUE)
  • Vignette typos and English improvements

networkABC 0.5-0

  • Added R_registerRoutines
  • Use R random numbers generation instead of rand and srand and the Rprintf
  • Use the Rprintf to direct C code outputs to the R console

networkABC 0.4-0

  • commented printf from abc_R.c, graph.c, network_random_R.C (CRAN requirement)
  • removed -Wunused-variable warnings

networkABC 0.3-0

  • bug fix to enable C code compatibility for macos

networkABC 0.2-0

  • vignette created

networkABC 0.1-1

  • Added readme, examples and website.
  • Code updated for R 3.5.2

networkABC 0.0-1

  • First release of the package.
  • Added a NEWS.md file to track changes to the package.

Reference manual

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install.packages("networkABC")

0.5-3 by Frederic Bertrand, 8 months ago


http://www-irma.u-strasbg.fr/~fbertran/, https://github.com/fbertran/networkABC


Report a bug at https://github.com/fbertran/networkABC/issues


Browse source code at https://github.com/cran/networkABC


Authors: Frederic Bertrand [cre, aut] , Myriam Maumy-Bertrand [aut] , Khadija Musayeva [ctb] , Nicolas Jung [ctb] , Université de Strasbourg [cph] , CNRS [cph]


Documentation:   PDF Manual  


GPL-3 license


Imports RColorBrewer, network, sna

Suggests PCIT, ggplot2, knitr


See at CRAN