causalDisturbance: Calculates enrichment analysis of KEGG pathways based on...

In pouryany/pathwayDisturbance: Pathway enrichment analysis of genomic using Causal Disturbance Analysis

Description

Calculates enrichment analysis of KEGG pathways based on causal disturbance model. For more information, see publication doi>10.1145/3107411.3107488

Usage

causalDisturbance(deIDs, allIDs, iter = 2000, alpha = 0.1, beta = 1,
  statEval = 1, fdrMethod = "BH", verbose = F)

Arguments

deIDs	a list of differentially expressed genes
allIDs	list of all genes in the experiment
iter	Iteration round for sampling causal disturbance
alpha	Decay factor for Source/Sink centrality, default 0.1.
beta	Relative importance of sink versus source
statEval	0 for summation of source/sink centrality 1 for product
fdrMethod	choice of false disovery rate method. inherited from p.adjust
verbose	printing pathway processing report

Value

list containing pathway names, number of pathway nodes and edges, Over-representation P-values, size of differentially expressed genes in the pathway, and causal disturbance

pouryany/pathwayDisturbance documentation built on Sept. 1, 2020, 12:13 a.m.