[BioC] R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)

[Steve Lianoglou]

> Thank you very much.
> Where can I get a glossary of the nomenclature used to query such  
> data bases ?
> As a physicist I have no idea what the values of attributes and  
> filters .... mean.
>

I'm not sure that there's one place you can go that will give you the  
full description of what each attribute means.

That having been said, you can get a list of names you can use as  
attributes/filters by using the `listAttributes` function, which will  
give you a data frame (~ 665 rows for humans) that give you an  
attribute to "human readable" map:

R> library(biomaRt)
R> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
R> head(listAttributes(hmart))
                             name                       description
1                ensembl_gene_id                   Ensembl Gene ID
2          ensembl_transcript_id             Ensembl Transcript ID
3             ensembl_peptide_id                Ensembl Protein ID
4 canonical_transcript_stable_id Canonical transcript stable ID(s)
5                    description                       Description
6                chromosome_name                   Chromosome Name
...

If you need more info than what's provided in the "description"  
column, you''ll have to do some hunting, or just ask on the list if  
you're getting stuck.

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos