SimEpiNEM: Compare algorithms.

In epiNEM: epiNEM

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)

epiNEM documentation built on Nov. 8, 2020, 6:51 p.m.