Hello,
I was following the excellent tutorial but when I get to this step
map <- select(org.Hs.eg.db, keys=unlist(mcols(kgConsensus)$gene_id), columns=c("SYMBOL"), keytype=c("ENTREZID")), I cannot figure out how to convert it to use with Arabidopsis, to "Collapse overlapping annotations". I am using atdb <- TxDb.Athaliana.BioMart.plantsmart28 rather than kgdb <- TxDb.Hsapiens.UCSC.hg19.knownGene but using org.At.tair.db instead of org.Hs.eg.db, but I get an error when I try that.
> map <- select(org.At.tair.db, keys=unlist(mcols(atConsensus)$gene_id), columns=c("SYMBOL"), keytype=c("ENTREZID"))
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.
Do you know a way around this or an alternative approach to collapse overlapping annotations that I could use for the Arabidopsis genome?
All the best,
James
Hello,
I was following the excellent tutorial but when I get to this step
map <- select(org.Hs.eg.db, keys=unlist(mcols(kgConsensus)$gene_id), columns=c("SYMBOL"), keytype=c("ENTREZID")), I cannot figure out how to convert it to use with Arabidopsis, to "Collapse overlapping annotations". I am usingatdb <- TxDb.Athaliana.BioMart.plantsmart28rather thankgdb <- TxDb.Hsapiens.UCSC.hg19.knownGenebut usingorg.At.tair.dbinstead oforg.Hs.eg.db, but I get an error when I try that.Do you know a way around this or an alternative approach to collapse overlapping annotations that I could use for the Arabidopsis genome?
All the best,
James