Dear all,
Good day to you. Would like to seek your help on two questions below. Thanks for your valuable time.
1) I run below scripts using compareCluster. However, even one gene map it gives output. Can we limit e.g. min three genes for each term (for KEGG as well)?
F0F1F1M_GO_BP <- compareCluster(F0F1F1M, fun="enrichGO", ont="BP", OrgDb=org.Rn.eg.db, pvalueCutoff=0.05, pAdjustMethod = "BH", minGSSize = 10, maxGSSize = 500, readable=TRUE) ; head(F0F1F1M_GO_BP)
Cluster ID Description GeneRatio BgRatio
1 LO_e GO:0006706 steroid catabolic process 2/10 26/18303
2 LG_eo GO:0032782 bile acid secretion 1/3 14/18303
3 LG_eo GO:0038183 bile acid signaling pathway 1/3 19/18303
4 LG_e GO:0032782 bile acid secretion 1/2 14/18303
5 LG_e GO:0038183 bile acid signaling pathway 1/2 19/18303
6 LG_e GO:0015721 bile acid and bile salt transport 1/2 31/18303
pvalue p.adjust qvalue geneID Count
1 8.670955e-05 0.03832562 0.020627745 Scarb1/Cyp24a1 2
2 2.293076e-03 0.04977891 0.016374640 Slc10a1 1
3 3.111182e-03 0.04977891 0.016374640 Slc10a1 1
4 1.529261e-03 0.03216469 0.001092180 Slc10a1 1
5 2.075141e-03 0.03216469 0.001092180 Slc10a1 1
6 3.384647e-03 0.03497468 0.001187595 Slc10a1 1
2) I would like to convert ID to symbol. But I faced problem in compareCluster using enrichKEGG.
F0F1F1M_KEGG <- compareCluster(F0F1F1M, fun="enrichKEGG", organism="rno", pvalueCutoff=0.05, pAdjustMethod="BH", minGSSize=10, maxGSSize=500) ; head(F0F1F1M_KEGG)
Cluster ID Description GeneRatio BgRatio
1 LO_eo rno04976 Bile secretion 3/11 94/8873
2 LO_e rno04976 Bile secretion 3/7 94/8873
3 LO_e rno05206 MicroRNAs in cancer 3/7 292/8873
4 LA_o rno04960 Aldosterone-regulated sodium reabsorption 1/1 38/8873
5 LA_o rno05143 African trypanosomiasis 1/1 40/8873
6 LA_o rno04370 VEGF signaling pathway 1/1 58/8873
pvalue p.adjust qvalue geneID Count
1 0.0001786577 0.0228681847 0.0208747409 24777/24646/25073 3
2 0.0000390834 0.0008598348 0.0005759659 24777/24646/25073 3
3 0.0011189312 0.0123082435 0.0082447564 24646/25279/100314163 3
4 0.0042826552 0.0238597224 0.0003587928 24680 1
5 0.0045080582 0.0238597224 0.0003587928 24680 1
6 0.0065366843 0.0238597224 0.0003587928 24680 1
F0F1F1M_KEGG_Sym <- setReadable(F0F1F1M_KEGG, OrgDb=org.Rn.eg.db, keyType="ENTREZID") Error in .testForValidKeys(x, keys, keytype, fks) : 'keys' must be a character vector
Thank you
