Question: Mapping gene symbols to gene names (org.Hs.eg.db?)
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gravatar for Tim Smith
5.1 years ago by
Tim Smith1.1k
Tim Smith1.1k wrote:
Hi, I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: -------------------------- library(org.Hs.eg.db) ### First two genes are ok... symbols <- c('JAK1','AATK','A2BP1','A2LD1') for(sym in symbols){     print('***')     entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA))     print(sym)     print(entrezid)     genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA))     print(genename) } ------------------------- I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? thanks. [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.1 years ago by James W. MacDonald50k • written 5.1 years ago by Tim Smith1.1k
Answer: Mapping gene symbols to gene names (org.Hs.eg.db?)
0
gravatar for James W. MacDonald
5.1 years ago by
United States
James W. MacDonald50k wrote:
Hi Tim, >symbols <- c('JAK1','AATK','A2BP1','A2LD1') >select(org.Hs.eg.db, symbols, c("ENTREZID","GENENAME"), "ALIAS") ALIAS ENTREZID GENENAME 1 JAK1 3716 Janus kinase 1 2 AATK 9625 apoptosis-associated tyrosine kinase 3 A2BP1 54715 RNA binding protein, fox-1 homolog (C. elegans) 1 4 A2LD1 87769 gamma-glutamylamine cyclotransferase Best, Jim On 5/13/2014 6:38 AM, Tim Smith wrote: > Hi, > > I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: > > -------------------------- > > library(org.Hs.eg.db) > > ### First two genes are ok... > symbols <- c('JAK1','AATK','A2BP1','A2LD1') > > for(sym in symbols){ > print('***') > entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA)) > print(sym) > print(entrezid) > > genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA)) > print(genename) > > } > > > ------------------------- > > I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? > > > thanks. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.1 years ago by James W. MacDonald50k
Thanks Jim! On Tuesday, May 13, 2014 10:18 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, >symbols <- c('JAK1','AATK','A2BP1','A2LD1') >select(org.Hs.eg.db, symbols, c("ENTREZID","GENENAME"), "ALIAS")   ALIAS ENTREZID                                          GENENAME 1  JAK1    3716                                    Janus kinase 1 2  AATK    9625              apoptosis-associated tyrosine kinase 3 A2BP1    54715 RNA binding protein, fox-1 homolog (C. elegans) 1 4 A2LD1    87769              gamma-glutamylamine cyclotransferase Best, Jim On 5/13/2014 6:38 AM, Tim Smith wrote: > Hi, > > I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example code below). However, during this process I can't get the gene names for some of the genes: > > -------------------------- > > library(org.Hs.eg.db) > > ### First two genes are ok... > symbols <- c('JAK1','AATK','A2BP1','A2LD1') > > for(sym in symbols){ >      print('***') >      entrezid <- as.character(mget(sym,org.Hs.egSYMBOL2EG,ifnotfound=NA)) >      print(sym) >      print(entrezid) > >      genename <- as.character(mget(entrezid,org.Hs.egGENENAME,ifnotfound=NA)) >      print(genename) > > } > > > ------------------------- > > I don't get any gene names for the last two genes in this example. Is there a better way of doing this? Perhaps with some other function/package? > > > thanks. > >     [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]
ADD REPLYlink written 5.1 years ago by Tim Smith1.1k
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