getAnnotation {maDB} | R Documentation |
This function retrieves annotation for a gene (or a list of genes) to different public repository IDs.
getAnnotation(id = NULL, con = NULL, method = "local", chip = NULL, v = TRUE, ...)
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. e.g. "hgu133plus2" should be submitted for the Affymetrix HG-U133plus2 chip. |
v |
If additional output should be written to the console. |
... |
additional parameters. |
A matrix where the rows correspond to the ids (genes) and the columns to the available annotations for the genes.
The local annotation using annotation packages is not implemented yet!
Johannes Rainer