Usage

  2. Usage:
  4.      enrichKEGG(
  5.        gene,
  6.        organism = "hsa",
  7.        keyType = "kegg",
  8.        pvalueCutoff = 0.05,
  9.        pAdjustMethod = "BH",
  10.        universe,
  11.        minGSSize = 10,
  12.        maxGSSize = 500,
  13.        qvalueCutoff = 0.2,
  14.        use_internal_data = FALSE
  15.      )
  17. Arguments:
  19.     gene: a vector of entrez gene id.
  21. organism: supported organism listed in
  22.           'http://www.genome.jp/kegg/catalog/org_list.html'
  24.  keyType: one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'
  26. pvalueCutoff: pvalue cutoff on enrichment tests to report
  28. pAdjustMethod: one of "holm", "hochberg", "hommel", "bonferroni", "BH",
  29.           "BY", "fdr", "none"
  31. universe: background genes. If missing, the all genes listed in the
  32.           database (eg TERM2GENE table) will be used as background.
  34. minGSSize: minimal size of genes annotated by Ontology term for
  35.           testing.
  37. maxGSSize: maximal size of genes annotated for testing
  39. qvalueCutoff: qvalue cutoff on enrichment tests to report as
  40.           significant.  Tests must pass i) ‘pvalueCutoff’ on unadjusted
  41.           pvalues, ii) ‘pvalueCutoff’ on adjusted pvalues and iii)
  42.           ‘qvalueCutoff’ on qvalues to be reported.
  44. use_internal_data: logical, use KEGG.db or latest online KEGG data

Example