SimEpiNEM {epiNEM} | R Documentation

## Compare algorithms.

### Description

Compares different network reconstruction algorithm on simulated data.

### Usage

    SimEpiNEM(
      runs = 10,
      do = c("n", "e"),
      random = list(FPrate = 0.1, FNrate = c(0.1, 0.5), single = 3, double = 1, reporters =
        10, replicates = 2),
      maxTime = FALSE,
      forcelogic = TRUE,
      epinemsearch = "greedy",
      bnemsearch = "genetic",
      ...
    )

### Arguments

`runs` | number simulation runs
`do` | string vector of algorithms to compare: e (epiNEM), n (Nested Effects Models), b (B-NEM), p (PC algorithm), a (Aracne), e.g. c("e", "n", "p")
`random` | list of false poitive rate FPrate, false negative rates FNrate, number of single knock-downs single, number of double knock-downs double, number of effect reporters reporters and number of replicates replicates
`maxTime` | TRUE if the algorithms are bound to a maximum running time in respect to epiNEM
`forcelogic` | if TRUE the randomly sampled ground truth network includes a complex logic with probability 1
`epinemsearch` | greedy or exhaustive search for epiNEM
`bnemsearch` | genetic or greedy search for B-NEM
`...` | additional parameters

### Value

returns list of specificity and sensitivity of inferred edges (spec, sens) and inferred expected data (spec2, sens2) and accuracy of logics (logics) and running time (time)

### Author(s)

Martin Pirkl

### Examples

    res <- SimEpiNEM(runs = 1)

[Package epiNEM version 1.16.0 Index]