Bgratio column in clusterProfiler enrichGO results
1
1
Entering edit mode
@mdtorohernando-11072
Last seen 7 weeks 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 • 2.1k views
ADD COMMENT
1
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 11 months 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.

ADD COMMENT

Login before adding your answer.

Traffic: 459 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6