sismonr (version 2.1.0)

summariseSimulation: Returns a summary data-frame of a simulation.

Description

Returns a summary data-frame of a simulation giving the maximum average abundance of each component over the different trials and the average abundance of the components at the final time of the simulation, for the selected in silico individuals.

Usage

summariseSimulation(
  simdf,
  inds = unique(simdf$Ind),
  trials = unique(simdf$trial),
  timeMin = min(simdf$time),
  timeMax = max(simdf$time),
  mergeAllele = T,
  mergePTM = T,
  mergeComplexes = F,
  verbose = T
)

Arguments

simdf

The data frame with the result of the simulation (see simulateInSilicoSystem).

inds

A vector of in silico individual names for which to compute the summary values.

trials

A vector of trials ID (= number) to use for the summary.

timeMin

Numeric. The minimum simulation time to take into account. Default value set to the minimum time in the simulation.

timeMax

Numeric. The maximum simulation time to take into account. Default value set to the maximum time in the simulation.

mergeAllele

Are the gene products originating from different alleles merged? Default TRUE. Also see mergeAlleleAbundance

mergePTM

Are the modified and non-modified versions of the proteins merged? Default TRUE. Also see mergePTMAbundance

mergeComplexes

Are the free and in complex gene products merged? Default FALSE. Also see mergeComplexesAbundance

verbose

If TRUE (default), print the individuals, trials, min and max time considered for the computation of the summary.

Value

A data-frame giving for each component (rows) and each individual (columns) the max and final average abundance over the different trials.

Examples

# NOT RUN {
mysystem = createInSilicoSystem(G = 5, regcomplexes = "none", ploidy = 2)
mypop = createInSilicoPopulation(15, mysystem)
sim = simulateInSilicoSystem(mysystem, mypop, 100, ntrials = 5)
summariseSimulation(sim$Simulation, c("Ind1", "Ind2", "Ind3", "Ind4"))
# }