inferPBN: Infer a Threshold PBN from a list of timeseries.

In davidkwca/inferTPBN: Infer Threshold PBNs from Timeseries Data.

Description

This is a wrapper for the whole inference procedure and makes use of innovateGeneUntilSaturated. For every gene it infers regulatory functions until the upper bound is reached or there is no more improvement from adding more functions.

Usage

inferPBN(ts.multi, p = 0.01, L.max = 2, n.cores = detectCores() - 1,
  seed = 111, partial = FALSE, verbal = FALSE)

Arguments

ts.multi	A list of timeseries.
p	The noise probability to use for the network.
L.max	The maximum number of regulatory networks to try to infer.
n.cores	The number of cores to be used.
seed	The random seed to use.
partial	Whether or not to *also* infer a network where only partial optimization over the last threshold parameter is performed. Defaults to FALSE.
verbal	Show progress report? Defaults to FALSE.

Value

A list containing the inferred network and the time taken to perform the inference.

See Also

FullRun

Examples

net.true <- createNetwork(inputProbabilities=c(0.5, 0.5), n=5, k=2)
ts.multi <- simulateNetwork(net.true, 10, 20)
inferred.list <- inferPBN(ts.multi, n.cores=1)
net.inferred <- inferred.list$net.inferred
time <- inferred.list$time.complete

davidkwca/inferTPBN documentation built on May 9, 2019, 12:53 p.m.