pvalueCutoff for enrichGO, enrichKEGG and enrichDO does not seem to function properly

Question

[t.mcgovern]

When setting the pvalueCutoff (0.01) for any of the enrich functions in clusterprofiler/DOSE the resulting object sitll contains results that have a p value >0.01 all the way up to 1.00! The same is also true for qvalueCutoff.

  cnet <- enrichKEGG(cnet_list, 
  pvalueCutoff = 0.01,
  pAdjustMethod = 'BH',
  minGSSize = 10)

   cnet_desc <- cnet@result[order(cnet@result$pvalue, decreasing = TRUE), ]

Note that I have removed multiple columns in cnet_desc to show the issues

head(cnet_desc)

    GeneRatio  BgRatio     pvalue p.adjust    qvalue
    105/5239   298/8840      1        1      0.5525544
    82/5239    368/8840      1        1      0.5525544
    28/5239    453/8840      1        1      0.5525544
    15/5239    73/8840       1        1      0.5525544
    127/5239   312/8840      1        1      0.5525544
    15/5239    71/8840       1        1      0.5525544

This is seriously impacting my analysis and I'm not sure how to fix it. Any help or suggesting would be appreciated!

Answer 1

[Bastien Hervé]

If I am not mistaken, all the cut offs are applied on the @result matrix to find pathways. So if you want to know which genes have been used in your KEGG enrichment, you have to filter yourself the @result matrix.