Batch query to map gene identifier to chromosome location using plant db

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benjamin • 0

@benjamin-20253

Last seen 5.1 years ago

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 • 338 views

ADD COMMENT • link 5.1 years ago benjamin • 0

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

ADD REPLY • link 5.1 years ago James W. MacDonald 65k

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sorry bout that. The plant species is Elaeis guineensis.

ADD REPLY • link 5.1 years ago benjamin • 0

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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 REPLY • link 5.1 years ago shepherl 3.8k

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