Usage

  1. Usage:
  3.      enrichGO(
  4.        gene,
  5.        OrgDb,
  6.        keyType = "ENTREZID",
  7.        ont = "MF",
  8.        pvalueCutoff = 0.05,
  9.        pAdjustMethod = "BH",
  10.        universe,
  11.        qvalueCutoff = 0.2,
  12.        minGSSize = 10,
  13.        maxGSSize = 500,
  14.        readable = FALSE,
  15.        pool = FALSE
  16.      )
  18. Arguments:
  20.     gene: a vector of entrez gene id.
  22.    OrgDb: OrgDb
  24.  keyType: keytype of input gene
  26.      ont: One of "BP", "MF", and "CC" subontologies, or "ALL" for all
  27.           three.
  29. pvalueCutoff: pvalue cutoff on enrichment tests to report
  31. pAdjustMethod: one of "holm", "hochberg", "hommel", "bonferroni", "BH",
  32.           "BY", "fdr", "none"
  34. universe: background genes. If missing, the all genes listed in the
  35.           database (eg TERM2GENE table) will be used as background.
  37. qvalueCutoff: qvalue cutoff on enrichment tests to report as
  38.           significant.  Tests must pass i) ‘pvalueCutoff’ on unadjusted
  39.           pvalues, ii) ‘pvalueCutoff’ on adjusted pvalues and iii)
  40.           ‘qvalueCutoff’ on qvalues to be reported.
  42. minGSSize: minimal size of genes annotated by Ontology term for
  43.           testing.
  45. maxGSSize: maximal size of genes annotated for testing
  47. readable: whether mapping gene ID to gene Name
  49.     pool: If ont='ALL', whether pool 3 GO sub-ontologies

Example