buildEntrezGeneDb {AnnotationDbi} | R Documentation |
These functions contact the NCBI eutils web services and then construct an organism (org.Xx.eg.db) database.
getGeneStuff(entrezGenes, dir="files") buildEntrezGeneDb(entrezGenes, file="test.sqlite") getEntrezGenesFromTaxId(taxId)
entrezGenes |
character vector of entrez Gene IDs that you want annotated. We presently check to make sure these are from the same species. You will get an error if they aren't. |
file |
file to write the database to. Traditionally these end with the .sqlite extension. |
dir |
directory for storing parsed XML. |
taxId |
A taxonomy ID from NCBI. You can browse these to select the species of interest from their website. |
In the case of getEntrezGenesFromTaxId
, this will be a
character vector of entrez gene IDs. In the case of
buildEntrezGeneDb
, then you will produce a SQLite database. In
the case of getGeneStuff
, then you get back a list of named lists
containing parsed XML values for each 800 long chunk of entrez Gene IDs.
## seems that some of the EGs are not from the taxid specified? (more tests) ## EGs <- getEntrezGenesFromTaxId(taxId) ## temporarily, lets use known EGs to run tests #library(org.Hs.eg.db) #EGs <- Lkeys(org.Hs.egCHR) #EGs <- EGs[c(1:10)] ## Obviously NOT a typical step. ## XML is broken, so I need a workaround for this. #system.time(buildEntrezGeneDb(EGs,file=tempfile())) #debug(getGeneStuff) #buildEntrezGeneDb(EGs,file=tempfile())