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Question: org.Hs.eg.db - convert ALIAS to ENTREZID, GENENAME
1
gravatar for Brian Smith
3.2 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

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!!

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Brian Smith120
2
gravatar for Martin Morgan
3.2 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Martin Morgan ♦♦ 22k
1
gravatar for Brian Smith
3.2 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Thanks! That worked!!

ADD COMMENTlink written 3.2 years ago by Brian Smith120
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