assess enrichment of the top networks

Usage

assess_enrichment(
  G = NULL,
  topList = NULL,
  ranks = NULL,
  X0Vector = NULL,
  type = c("ora", "gsea"),
  k = 99,
  minComponentSize = 2,
  minNetSize = 10,
  minKNes = 10,
  BPPARAMGsl = NULL,
  BPPARAMK = NULL
)

Arguments

G: igraph object
topList: ranked list of vertex names that will be used to define top networks
ranks: ranks of topList that will be assessed
X0Vector: named numeric vector that will be tested with GSEA or ORA. In case of GSEA it will be ranked by decreasing orderg, while in the case of ORA the names of the X0 values grater than 0 will be tested for enrichment, while all X0 names will be the universe.
type: gsea or ora
k: number of permutations
minComponentSize: size of the smallest graph component
minNetSize: minimum network size
minKNes: minimum k for considering a NES "confident"
BPPARAMGsl: BiocParallelParam instance to parallelize over gene sets. See BiocParallel::bplapply()
BPPARAMK: BiocParallelParam instance to paralleliz over permutations. BiocParallel::bplapply()