On Sun, Feb 6, 2011 at 8:02 AM, Mao Jianfeng <jianfeng.mao@gmail.com> wrote: > Thanks a lot. > > That may be good choice for me to download the annotation files. Do > you think I may refer to section 8 (Local BioMart databases) in the > the vignette? The section 8 for local databases is a little not enough > for me. It is too restricted for me. But, I will try and go deep by > it. > > Hi, Jian-Feng. It is always best to include the list in responses so that you get the best answers possible and everyone can benefit from your queries. I would not recommend installing a local biomart database, no. Follow the vignette, section 1. However, you will want to use phytozome_mart instead of ensembl. Give that a try and let us know where you have problems. Remember to include code and sessionInfo(). Sean 2011/2/6 Sean Davis <sdavis2@mail.nih.gov>: > > > > > > 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 > > > > -- > Jian-Feng, Mao > > the Institute of Botany, > Chinese Academy of Botany, > [[alternative HTML version deleted]]