innovateGeneUntilSaturated: Add new genes to regulatory set until no more improvement is...

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

Description

Greedily add regulatory functions to explain a gene's time progression.

Usage

innovateGeneUntilSaturated(ts.multi, net, g, partial = FALSE, verbal = TRUE,
  thresh = 0.1, k.max = 3)

Arguments

ts.multi	A list of timeseries.
net	A network.
g	A gene.
partial	Whether optimization of threshold parameter a is done only for latest gene. Defaults to FALSE.
verbal	Whether progress messages should be displayed.
thresh	By how much the improvement has to be to count. This has to be greater than zero as otherwise new genes will always be added to the brim.
k.max	How many regulatory genes to allow maximally. To avoid excessive computation, this should be set to a small constant. Defaults to 3.

Details

Genes are added until no more improvement is made or the upper limit is reached. In biological networks, a common assumption for the an upper bound on the number of inputs is in the range 3-5.

Value

A network.

See Also

innovateGene innovateGeneFunction

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