Question: Batch query to map gene identifier to chromosome location using plant db
0
gravatar for benjamin
8 months ago by
benjamin0
benjamin0 wrote:

I have a list differentially expressed proteins with Entrez Gene ID. I would like to map these Gene ID to the chromosome location (start and stop) using R. Is there a package for this?

annotation • 117 views
ADD COMMENTlink written 8 months ago by benjamin0

Probably, but unless you divulge the plant species how could anybody help?

ADD REPLYlink written 8 months ago by James W. MacDonald52k

sorry bout that. The plant species is Elaeis guineensis.

ADD REPLYlink written 8 months ago by benjamin0

I know there is an AnnotationHub resource for Elaeis guineensis but I think it would only provide the chromosome not start and stop.

library(AnnotationHub)
ah = AnnotationHub()
query(ah, "guineensis")
temp = query(ah, "guineensis")[[1]]
ids = head(keys(temp, keytype="ENTREZID"))
select(temp, keys=ids, columns=c("CHR"), keytype="ENTREZID")
ADD REPLYlink written 8 months ago by shepherl ♦♦ 1.7k
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