[BioC] Human, Mouse and Rat homologs

[David Lyon]

Hi Steffen

Thank you very much that works nicely and also thanks to everyone for their help and time.





----- Original Message ----
From: Steffen Durinck <sdurinck at lbl.gov>
To: David Lyon <david_lyon3 at yahoo.com>
Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
Sent: Thu, May 20, 2010 6:56:04 PM
Subject: Re: [BioC] Human, Mouse and Rat homologs

Hi David,

To get all ensembl_gene and ensembl_transcript ids you would need to do:

ids =getBM(c("ensembl_gene_id","ensembl_transcript_id"), mart=human)

Your other question, to get all attributes is unreasonable.  There are
more than a hundred attributes for human and this would be a huge
amount of data and I'm sure you don't need all of it.  Also, biomaRt
and the BioMart system won't allow you to query for all attributes at
once.  It is better to select the attributes you really need.
If you really need everything you'd be better of downloading a mysql
dump of Ensembl human from the Ensembl website.

Cheers,
Steffen

On 5/20/10, David Lyon <david_lyon3 at yahoo.com> wrote:
> Hi Michael and Wolfgang
>
> Thanks for your help, I think I can get what I need.I am new to R and
> therefore apologizes for the simple q's.
>
> A couple last questions on this thread if I may:
>
> if I wanted all the gene ids from ensembl it would be this:
> entrez =getBM("ensembl_gene_id", mart=human)
>> entrez
>
> but how can I get the following working and return all the gene_ids and
> transcript_ids?
> entrez =getBM("ensembl_gene_id","ensembl_transcript_id", mart=human)
>
>
> My final question is there a wild card '*' , essentially give me all the
> attributes returns for human ensembl eg:
> entrez =getBM(*, mart=human)
>
>
>
> Thanks again!
>
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