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malhamdoosh / EGSEA

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.
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Error in initialize(value, ...): l'argomento "go_id" non è specificato e non ha un valore predefinito #14

Open Francesco1993 opened 6 years ago

Francesco1993 commented 6 years ago

Error in initialize(value, ...): l'argomento "go_id" non è specificato e non ha un valore predefinito Traceback:

  1. buildIdx(entrezIDs = orthologs_biomarkers_monkey_delta_entrez_human$entrezgene_human, . species = "human", gsdb.gsets = "all", msigdb.gsets = "none", . kegg.exclude = c("Metabolism"))
  2. buildGeneSetDBIdx(entrezIDs = entrezIDs, species = species, geneSets = gsdb.gsets, . go.part = go.part, min.size = min.size)
  3. xx[[go.terms[i]]]
  4. xx[[go.terms[i]]]
  5. .doubleBracketSub(x, i, j, ...)
  6. mget(i, envir = x, ifnotfound = NA)
  7. mget(i, envir = x, ifnotfound = NA)
  8. as.list(envir)
  9. as.list(envir)
  10. .toListOfLists(y, mode = 1, makeGONode)
  11. do.call(FUN, slice_one)
  12. do.call(FUN, slice_one)
  13. (function (go_id, Term, Ontology, Definition, ...) . { . new("GOTerms", GOID = go_id[1], Term = Term[1], Ontology = Ontology[1], . Definition = Definition[1], ...) . })(go_id..2 = c("GO:0032201", "GO:0032201", "GO:0032201"), Term = c("telomere maintenance via semi-conservative replication", . "telomere maintenance via semi-conservative replication", "telomere maintenance via semi-conservative replication" . ), Ontology = c("BP", "BP", "BP"), Definition = c("The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication.", . "The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication.", . "The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication." . ), Synonym = c("equal telomere replication", "telomeric fork progression", . "telomeric replication fork progression"), Secondary = c(NAcharacter, . NAcharacter, NAcharacter))
  14. new("GOTerms", GOID = go_id[1], Term = Term[1], Ontology = Ontology[1], . Definition = Definition[1], ...)
  15. initialize(value, ...)
  16. initialize(value, ...)
Francesco1993 commented 6 years ago

Hello, I'm trying to use your package but I don't know why it behaves in this way and I'm not able to perform ORA. Am I doing something wrong? Thank you. Francesco

P.S. this is the code that I'm using: gs.annot <- buildIdx(entrezIDs = orthologs_biomarkers_monkey_delta_entrez_human$entrezgene_human, species = "human", gsdb.gsets = "all")