library(PCSF)data("STRING")data("Tgfb_phospho")ppi <- construct_interactome(STRING)ppiterminals <- Tgfb_phosphostr(terminals)subnet <- PCSF(ppi, terminals, w = 2, b = 1, mu = 0.0005)library(topGO)gene_universe <- V(ppi)$nameres <- enrichment_analysis(subnet, mode=1, gene_universe)
resulted in:
Error in which(sapply(enrichment_tab$Genes, function(x) length(unlist(strsplit(x, : argument to 'which' is not logical In addition: Warning messages: 1: In cluster_edge_betweenness(subnet) : At community.c:460 :Membership vector will be selected based on the lowest modularity score. 2: In cluster_edge_betweenness(subnet) : At community.c:467 :Modularity calculation with weighted edge betweenness community detection might not make sense -- modularity treats edge weights as similarities while edge betwenness treats them as distances
library(PCSF)data("STRING")data("Tgfb_phospho")ppi <- construct_interactome(STRING)ppiterminals <- Tgfb_phosphostr(terminals)subnet <- PCSF(ppi, terminals, w = 2, b = 1, mu = 0.0005)library(topGO)gene_universe <- V(ppi)$nameres <- enrichment_analysis(subnet, mode=1, gene_universe)resulted in:
Error in which(sapply(enrichment_tab$Genes, function(x) length(unlist(strsplit(x, : argument to 'which' is not logical In addition: Warning messages: 1: In cluster_edge_betweenness(subnet) : At community.c:460 :Membership vector will be selected based on the lowest modularity score. 2: In cluster_edge_betweenness(subnet) : At community.c:467 :Modularity calculation with weighted edge betweenness community detection might not make sense -- modularity treats edge weights as similarities while edge betwenness treats them as distancesI think enrichment_tab$Genes is missing from enrichment_tab, when running enrichment_analysis(). https://github.com/IOR-Bioinformatics/PCSF/blob/4e5f2707fdd096b760e5bb4ca60938a3c9836d78/R/enrichment_analysis.R#L150