getAnnotation {maDB}R Documentation

Annotate a gene

Description

This function tries to retrieve the annotation for a gene (or a list of genes) to different public repository IDs.

Usage

getAnnotation(id = NULL, con = NULL, method = "local", chip = NULL, v = TRUE, ...)

Arguments

id The gene ID (or IDs), for example Affymetrix probe set IDs, GenBank IDs...
con The database connection to the "maDB" database, if method is "db". If the annotation should be done using the ensembl mart database using the biomaRt package the mart connection object should be submitted with con. If local annotation (for example using Bioconductors Annotation packages) should be used this atribute can be omitted.
method The annotation method, one of c("local","db","mart").
chip An identifier for the chip or package that should be used to annotate the id. For the Affymetrix HG U133plus2 chip for example "hgu133plus2" should be submitted.
v If additional output should be written to the console.
... additional parameters.

Value

A matrix where the rows correspond to the ids (genes) and the columns the available annotations for the genes.

Warning

The local annotation using annotation packages is not implemented yet!

Author(s)

Johannes Rainer

See Also

dbGetAnnotation


[Package maDB version 1.8.0 Index]