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. 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/ -- Jian-Feng, Mao

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 [[alternative HTML version deleted]]