On Sun, Feb 6, 2011 at 7:15 AM, Mao Jianfeng <jianfeng.mao@gmail.com> wrote:

> Dear lister,
>
> I am new to bioconductor and genomics, coming from classical
> statistics using R. Now, I am working on population genomics of a
> plant species Arabidopsis lyrata.
>
> I would like to using biomaRt library to get my genomic variant (snp,
> indel, CNV) in VCF4.0 format annotated by the available
> gene/protein/pathway annotations of Arabidopsis lyrata stored in
> Pytozome (http://www.phytozome.net/search.php) by using biomaRt
> package.
>
> I have read the manual of biomaRt package. But, unfortunately, the
> example of biomaRt is only for Human which is different to a plant.
> Now, I lost my directions of using biomaRt package, for example how to
> link to phytozome, how to choose the right dataset for annotation.
>
> Could you please show me some lines of R code to let me start? I can
> not reach any helps around me.
>
>
Take a look at the vignette.  Section 6 shows connecting to marts other than
ensembl.  You'll want to be familiar with the biomart interface to phytozome
before using the biomaRt R package.  In other words, use the web version
first.  Feel free to write back with your code and an output of
sessionInfo() if you have problems after reading the vignette.

I should mention that biomaRt is not going to return your data in VCF4
format.  The data are always returned as a data.frame and VCF4 cannot be
easily encapsulated in a single data.frame.


> Looking forward to hearing from you. Thanks in advance.
>
> the phytozome websit for annotation data of Arabidopsis lyrata:
> ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v6.0/Alyrata/annotation/
>
>
You can use R to download these files directly.  See ?download.file or the
RCurl package.

Sean

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