enricher.R

library(clusterProfiler)
library(DT)
library(tibble)

pathway <- character(0)
cids <- list()

for(i in 1:length(mset_SMPDB_format_KEGG)) {
  row = mset_SMPDB_format_KEGG[[i]]
  pathway <- c(pathway, row[[2]])
  cids[[i]] <- row[[3]]
}

tb <- tibble(pathway=pathway, cID=cids)
y <- enricher(kusano, pvalueCutoff=0.5, TERM2GENE=tb, minGSSize=1, qvalueCutoff = 0.5)
DT::datatable(as.data.frame(y))

for (i in 1:length(mset_SMPDB_format_KEGG)){
  if (mset_SMPDB_format_KEGG[[i]][[1]] == "SMP00493") {
    print(mset_SMPDB_format_KEGG[[i]][[2]])
    print(intersect(kusano, mset_SMPDB_format_KEGG[[i]][[3]]))
    #print(mset_SMPDB_format_KEGG[[i]][[3]])
  }
}