Bgratio column in clusterProfiler enrichGO results
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@mdtorohernando-11072
Last seen 2.9 years ago
Spain

I have a doubt regarding the column Bgratio obtained in the clusterProfiler R package after enrichGO function. I have used the following code:

ego.BP <- enrichGO(gene = genes$Id, universe = universe, keytype = 'ENSEMBL', OrgDb = org.Mm.eg.db, ont = 'BP', pAdjustMethod = 'BH', pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = T)

and I obtained the following result:

  Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
1 acylglycerol metabolic process 10/128 101/20854 6,37E-010 7,70E-007 6,79E-007 Ces1d/Thrsp/Apoa5/Dgat2/Slc37a4/Lpin1/Gpx1/Fitm2/Lpin2/Ces1g 10
2 neutral lipid metabolic process 10/128 103/20854 7,74E-010 7,70E-007 6,79E-007 Ces1d/Thrsp/Apoa5/Dgat2/Slc37a4/Lpin1/Gpx1/Fitm2/Lpin2/Ces1g 10
3 lipid homeostasis 10/128 118/20854 2,96E-009 1,76E-006 1,55E-006 Angptl4/Apoa5/Cyp7a1/Dgat2/Slc37a4/Abcg8/Lipg/Hpn/Fitm2/Nr1h4 10
4 triglyceride metabolic process 9/128 88/20854 3,53E-009 1,76E-006 1,55E-006 Thrsp/Apoa5/Dgat2/Slc37a4/Lpin1/Gpx1/Fitm2/Lpin2/Ces1g 9
5 cholesterol homeostasis 8/128 69/20854 9,87E-009 3,27E-006 2,89E-006 Apoa5/Cyp7a1/Dgat2/Slc37a4/Abcg8/Lipg/Hpn/Nr1h4 8
6 sterol homeostasis 8/128 69/20854 9,87E-009 3,27E-006 2,89E-006 Apoa5/Cyp7a1/Dgat2/Slc37a4/Abcg8/Lipg/Hpn/Nr1h4 8


I would like to know how the Bgratio is calculated and its utility.

Thanks in advance,

María

 

 

clusterprofiler • 4.4k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 11 days ago
China/Guangzhou/Southern Medical Univer…

please refer to the vignette <https://www.bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/DOSE.html#do-term-enrichment-analysis>.

 

Referring to the equation of how pvalue was calculated, BgRatio = M/N.

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Could we add BgRatio for groupGO results? I need this information for groupGO function. It would be nice if there is any possibility you could suggest to me. Thank you very much!

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