Showing more terms in the result of GESA by ClusterProfiler

Question

[ytlin610]

Hi

I've been working on the gene set enrichment analysis by ClusterProfiler, and I'm able to generate the enriched terms table by the enricher function:

CRE_MapMan_GSEA <-enricher(DEG_cht7_6_up_LocusID$Gene_ID,
                           TERM2GENE=TERM2GENE, 
                           TERM2NAME = TERM2NAME,
                           pvalueCutoff = 0.05)

Result:

  ID               Description                              pvalue

    28.1           DNA.synthesis/chromatin structure        6.96E-19
    31.6.1.1       cell.motility.eukaryotes.basal bodies    4.77E-08
    28.2           cell.motility.eukaryotes.basal bodies    1.63E-06
    24             DNA.repair                               4.38E-06
    31.2           Biodegradation of Xenobiotics            1.32E-05
    27.3.44        cell.division                            1.90E-03
    31.1           RNA.regulation of transcription.         2.24E-03
                   Chromatin Remodeling Factors

However, there're only 7 terms displayed. Does that mean the rest of them are not significant enough? Is there any way I can see the p-values of more terms? I've tried to play with the pvalueCutoff parameter, but the number of the displayed term is still the same.

Thanks!

Answer 1

[Guangchuang Yu]

Try to use different qvalueCutoff value as cut off.

[ytlin610]

It worked! Thank you very much!