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@niranjanshirgaonkar-15284
Last seen 6.7 years ago
Hi
I was trying to do KEGG and GO analysis in R using clusterProfiler.
rm(list = ls()) dev.off() library(clusterProfiler) library(org.Hs.eg.db) x <- "ENSG00000183733" # human figla x.df <- bitr(x, fromType = "ENSEMBL", toType = c("ENSEMBL", "ENTREZID", "SYMBOL"), OrgDb = org.Hs.eg.db) gene1 <- x.df$ENTREZID ggo <- groupGO(gene = gene1, OrgDb = org.Hs.eg.db, ont = "CC", level = 3, readable = TRUE) # This works great. ########### ########### y <- "ENSDARG00000087166" # zebrafish figla y.df <- bitr(y, fromType = "ENSEMBL", toType = c("ENSEMBL", "ENTREZID", "SYMBOL"), OrgDb = org.Hs.eg.db) Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.
Does the same method not work with Zebrafish? Please guide me.
Apologies and thank you!
Here is the list of all annotation packages http://bioconductor.org/packages/3.6/data/annotation/ for anyone like me who might have problems with this.