setReadable error in ClusterProfiler
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Entering edit mode
5 months ago
WF • 0

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

error setReadable clusterProfiler • 206 views
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