Description Usage Arguments Value Author(s) Examples

View source: R/estimateNetwork.R

Given a biRte model, this function makes posterior inference about possible upstream-downstream relationships between active regulators. This is done based on observed differential expression of putative target genes. The idea is that regulator A acts upstream of regulator B, if differentially expressed targets of B are a subset of those of A.

1 2 | ```
estimateNetwork(model, thresh=0.1, select=c("marginal", "MAP"), method="pairwise",
de.genes, bootstrap=0, typeII=0.1)
``` |

`model` |
biRte model |

`thresh` |
cutoff for marginal posterior probabilities |

`select` |
"marginal": select regulators based on marginal posterior probabilities; "MAP": select regulators based on MAP configuration |

`method` |
algorithm used for NEM based network inference, see |

`de.genes` |
set of differentially expressed genes |

`bootstrap` |
optional: number of bootstrap replicates to draw (non-parameteric bootstrap) |

`typeII` |
assumed type-II error rate |

nem-model

Holger Froehlich

1 | ```
# see vignette
``` |

birte documentation built on May 31, 2017, 1:41 p.m.

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