bestRanking: Identify the best ranking

In metaboGSE: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

Description

This function computes the performance indices of different rankings compared to the random ranking for gene removal and identify the best ranking

Usage

bestRanking(fns)

Arguments

fns	List of fitness objects.

Value

The performance indices for all rankings and the best ranking.

Examples

data(Ec_core)
mod <- rescue(Ec_core, target=0.1)
mod.weight <- changeObjFunc(mod$rescue, react=rownames(mod$coef), obj_coef=mod$coef)
ranks <- list(
   rep.1=data.frame(
       expr=setNames(rnorm(length(sybil::allGenes(mod.weight)), mean=5, sd=4),
           sybil::allGenes(mod.weight))),
   rep.2=data.frame(
       expr=setNames(rnorm(length(sybil::allGenes(mod.weight)), mean=5, sd=4.1),
           sybil::allGenes(mod.weight))))
fn <- fitness(model=mod.weight, ranks=ranks, step=200, draw.num=1)
bestRanking(list(fn))

metaboGSE documentation built on Oct. 23, 2020, 8:14 p.m.