org.Hs.eg.db - convert ALIAS to ENTREZID, GENENAME
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Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 4.2 years ago
United States

Hi,

I used to convert gene aliases to entrez ids etc with the following code:

mysymbols <- c("TLR4",  "STAT3")

library("org.Hs.eg.db")
matx <- maty <- select(org.Hs.eg.db, keys=mysymbols, columns=c("ENTREZID","GENENAME"), keytype="ALIAS")

Now, I get an error:

Error in select(org.Hs.eg.db, keys = mysymbols, columns = c("ENTREZID",  : 
  unused arguments (keys = gsymbols2, columns = c("ENTREZID", "GENENAME"), keytype = "ALIAS")

Has something changed in the package/select method? Am I doing something wrong?

thanks!!

org.hs.eg.db select • 5.8k views
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3
Entering edit mode
@martin-morgan-1513
Last seen 4 months ago
United States

Probably another package has defined a select() function; try

AnnotationDbi::select(org.Hs.eg.db, keys=mysymbols,   
    columns=c("ENTREZID","GENENAME"), keytype="ALIAS")

The output of sessionInfo() is always helpful for further diagnosis.

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1
Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 4.2 years ago
United States

Thanks! That worked!!

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