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rabico_practice_2019_clusterProfiler

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Mar 20th, 2019
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  1. library(clusterProfiler)
  2. library(org.Hs.eg.db)
  3. data(geneList, package="DOSE")
  4. x <-c("ENSG00000221963","ENSG00000157601","ENSG00000100342","ENSG00000128284","ENSG00000183486","ENSG00000239713","ENSG00000184979","ENSG00000185753","ENSG00000128335","ENSG00000128203","ENSG00000089472","ENSG00000157551","ENSG00000185022","ENSG00000128394","ENSG00000100226","ENSG00000025708","ENSG00000179750","ENSG00000100234","ENSG00000169933","ENSG00000158290","ENSG00000154734","ENSG00000102081","ENSG00000100345","ENSG00000102265","ENSG00000099998","ENSG00000100219","ENSG00000142173","ENSG00000182871","ENSG00000196924","ENSG00000159228","ENSG00000102218","ENSG00000159200","ENSG00000101911","ENSG00000128342","ENSG00000100258","ENSG00000142156","ENSG00000159231","ENSG00000155304","ENSG00000100299","ENSG00000008086","ENSG00000130066","ENSG00000128165","ENSG00000102317","ENSG00000147050","ENSG00000185339","ENSG00000154736","ENSG00000075218","ENSG00000244509","ENSG00000160255","ENSG00000147027","ENSG00000182220","ENSG00000157557","ENSG00000165259","ENSG00000155313","ENSG00000156500","ENSG00000102158","ENSG00000184205","ENSG00000180530","ENSG00000186871","ENSG00000099968","ENSG00000072501","ENSG00000101955","ENSG00000183778","ENSG00000233521","ENSG00000102034","ENSG00000102024","ENSG00000142197","ENSG00000102359","ENSG00000100196","ENSG00000100297","ENSG00000198951","ENSG00000171155","ENSG00000206195","ENSG00000171388","ENSG00000073146","ENSG00000133138","ENSG00000101825","ENSG00000147202","ENSG00000090889","ENSG00000100225","ENSG00000177485","ENSG00000101974","ENSG00000128228","ENSG00000131171","ENSG00000160211","ENSG00000075234","ENSG00000147065","ENSG00000235513","ENSG00000183255","ENSG00000100106","ENSG00000125354","ENSG00000102144","ENSG00000130150","ENSG00000172534","ENSG00000101935","ENSG00000184164","ENSG00000198089","ENSG00000100393","ENSG00000100065","ENSG00000189060","ENSG00000281383","ENSG00000188153","ENSG00000100084","ENSG00000198862","ENSG00000154640","ENSG00000184809","ENSG00000203650","ENSG00000160200","ENSG00000159140","ENSG00000101888","ENSG00000147044","ENSG00000128272","ENSG00000173276","ENSG00000184083","ENSG00000005889","ENSG00000125676","ENSG00000234883","ENSG00000160219","ENSG00000147130","ENSG00000159259","ENSG00000147206","ENSG00000169184","ENSG00000130962","ENSG00000100003","ENSG00000123131","ENSG00000101856","ENSG00000157617","ENSG00000068400","ENSG00000183067","ENSG00000183530","ENSG00000183765","ENSG00000280383","ENSG00000177663","ENSG00000102221","ENSG00000101871","ENSG00000100280","ENSG00000100354","ENSG00000175302","ENSG00000160216","ENSG00000182240","ENSG00000156299","ENSG00000093009","ENSG00000100092","ENSG00000101966","ENSG00000100105","ENSG00000099917","ENSG00000100162","ENSG00000236393","ENSG00000100058","ENSG00000243646","ENSG00000068323","ENSG00000234703","ENSG00000122126","ENSG00000068366","ENSG00000170965","ENSG00000157542","ENSG00000101986","ENSG00000236830","ENSG00000244486","ENSG00000233382","ENSG00000180957","ENSG00000242247","ENSG00000056277","ENSG00000188706","ENSG00000102384","ENSG00000100242","ENSG00000169093","ENSG00000235636","ENSG00000272872","ENSG00000093000","ENSG00000131263","ENSG00000160209","ENSG00000100097","ENSG00000013619","ENSG00000128294","ENSG00000231010","ENSG00000182944","ENSG00000100109","ENSG00000159256","ENSG00000094841","ENSG00000196576","ENSG00000006756","ENSG00000189306","ENSG00000275793","ENSG00000234062","ENSG00000165195","ENSG00000101972","ENSG00000101945","ENSG00000128262","ENSG00000082458")
  5.  
  6.  
  7. ids <- bitr(x, fromType="ENSEMBL", toType="ENTREZID", OrgDb="org.Hs.eg.db")
  8. head(ids)
  9.  
  10. egoCC <- enrichGO(gene  = ids$ENTREZID,OrgDb     = org.Hs.eg.db,ont       = "CC",pAdjustMethod = "fdr",pvalueCutoff  = 0.01,qvalueCutoff  = 0.05,readable      = TRUE)
  11.  
  12. egoMF <- enrichGO(gene          = ids$ENTREZID,OrgDb         = org.Hs.eg.db,ont           = "MF",pAdjustMethod = "fdr",pvalueCutoff  = 0.01,qvalueCutoff  = 0.05,readable      = TRUE);
  13.  
  14. egoBP <- enrichGO(gene          = ids$ENTREZID,OrgDb         = org.Hs.eg.db,ont           = "BP",pAdjustMethod = "fdr",pvalueCutoff  = 0.01,qvalueCutoff  = 0.05,readable      = TRUE);
  15.  
  16. kk <- enrichKEGG(gene        = ids$ENTREZID, organism     = 'hsa',pvalueCutoff = 0.05)
  17.  
  18. barplot(egoCC)
  19.  
  20. barplot(egoMF)
  21.  
  22. barplot(egoBP)
  23.  
  24. barplot(kk)
  25.  
  26.  
  27. dotplot(egoCC)
  28.  
  29. dotplot(egoMF)
  30.  
  31. dotplot(egoBP)
  32.  
  33. dotplot(kk)
  34.  
  35. emapplot(egoCC)
  36.  
  37. emapplot(egoMF)
  38.  
  39. emapplot(egoBP)
  40.  
  41. emapplot(kk)
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