dbGetAnnotation {maDB}R Documentation

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

Description

dbGetAnnotation returns the annotation of the submitted IDs to available annotations in the maDB annotation database table. For an example refer to the package vignette (which can be opened using the openMadbVignette function).

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 The connection to the maDB database (created using the dbConnect function from the RdbiPgSQL package).
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 database table can be easily created in a PostgreSQL database using the dbUpdateAnnotation function.

Author(s)

Johannes Rainer

References

See Also

dbUpdateAnnotation dbGetExperimentInfo loadFromDB


[Package maDB version 1.10.0 Index]