calImportance: Computing the importance of each prime implicant

In ningshi/ATEN: ATEN

Description

A helper function for computing the importance of each prime implicant in a forest

Usage

calImportance(input, resp, forest)

Arguments

input	A dataset matrix containing all gene expression. Each value corresponds to a gene expression of an input gene at a certain time point t.
resp	A vector containing the gene expression of the target gene.
forest	A set of And/Or trees, each tree is a list

Value

a vector includes the importances, the order of the importances corresponds to the order of prime implicants in the forest

References

Müssel, Christoph, Martin Hopfensitz, and Hans A. Kestler. "BoolNet—an R package for generation, reconstruction and analysis of Boolean networks." Bioinformatics 26.10 (2010): 1378-1380.

See Also

generateRandomNKNetwork

Examples

##Generate a random Boolean network
net1<-generateRandomNKNetwork(n=10, k=5, topology="scale_free",linkage="uniform",simplify=TRUE,readableFunctions=TRUE)

##Build the time-series data
datalist<-buildTimeSeries(net1,2,5,0)

##Select the first node as target gene and find 5 putative predictive And/Or trees using very simple parameters
datalist[[3]]<-datalist[[3]][,1]
forest<-lapply(rep(1,5),function(x){saalg(datalist,8,NULL,-2,-1,200)})

##To see all prime implicants in the forest
PIs<-unique(unlist(forest,recursive = F))
Importances<-calImportance(datalist[[2]],datalist[[3]],forest)
print(PIs)
print(Importances)

ningshi/ATEN documentation built on April 27, 2021, 7:40 a.m.