Search
Question: org.Hs.eg.db - convert ALIAS to ENTREZID, GENENAME
1
gravatar for Brian Smith
2.2 years ago by
Brian Smith90
United States
Brian Smith90 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 2.2 years ago • written 2.2 years ago by Brian Smith90
2
gravatar for Martin Morgan
2.2 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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 2.2 years ago • written 2.2 years ago by Martin Morgan ♦♦ 20k
1
gravatar for Brian Smith
2.2 years ago by
Brian Smith90
United States
Brian Smith90 wrote:

Thanks! That worked!!

ADD COMMENTlink written 2.2 years ago by Brian Smith90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 299 users visited in the last hour