simulateTN: Cut and simulation of a boolean model at t1

In CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This function cuts a model according to a bitstring optimised at T1, and simulates the model accordingly.

Usage

simulateTN(CNOlist, model, bStrings)

Arguments

CNOlist	a CNOlist object
model	a full model
bStrings	a bitstring to cut the model, as output by gaBinaryT1 (i.e. a vector of 1s and 0s, of length equal to the number of reactions in the model)

Details

This function is a wrapper around the family of functions called simulatorT1 , T2 and TN.

Value

a matrix of simulated values, including all species in the model, i.e. to be used as input of gaBinaryTN.

Author(s)

T.Cokelaer, S.Schrier based on simulatorT1 (C.Terfve)

See Also

cutAndPlotResultsT1, simulatorT1

Examples

# This will compute the output of a random model obtained by randomly selecting
# which gates of the initial models are included.

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")

simRes<-simulateTN(
	CNOlist=CNOlistToy, 
	model=ToyModel, 
	bStrings=list(round(runif(length(ToyModel$reacID)))))

Example output

Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.