dbGetAnnotation {maDB} | R Documentation |
dbGetAnnotation
this function can be used to annotate a list of ids (for example Affymetrix IDs) using a formerly created annotation database.
dbGetAnnotation(Con,id,columns=c("gen_bank","description","uni_gene","locuslink","symbol","chromosome"),chip=NULL,search.col="id",v=TRUE,quickload=FALSE)
Con |
A connection object (create it with the dbConnect.PgSQL.conn function from the package RdbiPgSQL) |
id |
The IDs of the genes that should be annotated. |
columns |
the identifier to which the submitted ids should be annotated. |
chip |
the chip (or for two color arrays a oligo set identifier) from which the ids were taken from (e.g. hgu133plus2 for the Affymetrix GeneChip 133Plus2). |
search.col |
In wich of the columns the ids submitted with the id parameter should be searched for. |
v |
If TRUE additional information will be printed to the console. |
quickload |
Only valid if id="id", the annotation data will be fetched much quicker from the database. |
The annotation table can be easily created in a PostgreSQL database using the dbUpdateAnnotation
function.
Johannes Rainer
dbUpdateAnnotation
dbGetExperimentInfo
dbConnect
loadFromDB