dbGetAnnotation {maDB}R Documentation

Annotate a list of IDs using the annotation table in the database.

Description

dbGetAnnotation this function can be used to annotate a list of ids (for example Affymetrix IDs) using a formerly created annotation database.

Usage

dbGetAnnotation(Con,id,columns=c("gen_bank","description","uni_gene","locuslink","symbol","chromosome"),chip=NULL,search.col="id",v=TRUE,quickload=FALSE)

Arguments

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.

Details

The annotation table can be easily created in a PostgreSQL database using the dbUpdateAnnotation function.

Author(s)

Johannes Rainer

References

See Also

dbUpdateAnnotation dbGetExperimentInfo dbConnect loadFromDB


[Package maDB version 1.2.0 Index]