I was just reminded that mget (an older, classic R approach) has been superseded by Marc Carlson's (modern, intuitive) "select" interface. Here it is in action: select(org.Hs.eg.db, geneIDs, "SYMBOL") ENTREZID SYMBOL 1 3765 KCNJ9 2 100126492 TRNAS-CGA 3 100873237 MTND2P32 4 9715 FAM131B 5 100271498 RPL34P22 6 bogus <na> On Jan 17, 2013, at 6:09 AM, Paul Shannon wrote: >> >> I am looking for a way to convert geneid to gene name. > > Hi Matt, > > This might be what you need: > > biocLite("org.Hs.eg.db") > library(org.Hs.eg.db) > # some sample entrez geneIDs; you will have your own source for these > geneIDs <- c("3765","100126492", "100873237", "9715","100271498", "bogus") > mget(geneIDs, org.Hs.egSYMBOL, ifnotfound=NA) > $`3765` > [1] "KCNJ9" > > $`100126492` > [1] "TRNAS-CGA" > > $`100873237` > [1] "MTND2P32" > > $`9715` > [1] "FAM131B" > > $`100271498` > [1] "RPL34P22" > > $bogus > [1] NA > > - Paul > > > On Jan 16, 2013, at 8:11 AM, Matthew Liebers wrote: > >> I am looking for a way to convert geneid to gene name. Specifically, I am >> calling for variants and then using VariantAnnotation to output using a >> predictCoding() function that gives the following columns: >> "seqnames" "ranges" "strand" | "paramRangeID" >> "varAllele" "CDSLOC" "PROTEINLOC" "QUERYID" >> "TXID" "CDSID" "*GENEID*" "CONSEQUENCE" "REFCODON" >> "VARCODON" "REFAA" "VARAA". >> >> I am interested in gene name moreso than GENEID and so I have been looking >> at how to do this including using the biomaRt package, but I was wondering >> whether anyone knew about this. Thanks in advance! >> >> Matt >> >> [[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 >