Question: Creating annotation packages
0
gravatar for Gábor Csárdi
10.6 years ago by
Gábor Csárdi60 wrote:
Dear All, I am trying to create an annotation package that contains predicted miRNA targets, basically it would be a mapping between Entrez Gene IDs and miRNA families, for a couple of organisms, together with some additional info or course. I am trying to make use of the AnnBuilder package, but could not find out whether it can do this at all or not. Btw. the vignettes of it seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not public any more. So my questions are: 1) Is AnnBuilder the right tool for this? 2) If not, are there any "right" tools? I don't mind creating the sqlite database by hand, but how do I create AnnDbBimap objects for it? 3) Are your scripts for building the standard annotation packages (e.g. org.xx.eg.db) publicly available somewhere? It would be of great help to see how this is done. Thanks, Gabor -- Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM
mirna annotation annbuilder • 492 views
ADD COMMENTlink modified 10.6 years ago by Sean Davis21k • written 10.6 years ago by Gábor Csárdi60
Answer: Creating annotation packages
0
gravatar for Sean Davis
10.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Fri, Jan 30, 2009 at 11:13 AM, Gábor Csárdi <gabor.csardi@unil.ch> wrote: > Dear All, > > I am trying to create an annotation package that contains predicted > miRNA targets, basically it would be a mapping between Entrez Gene IDs > and miRNA families, for a couple of organisms, together with some > additional info or course. > > I am trying to make use of the AnnBuilder package, but could not find > out whether it can do this at all or not. Btw. the vignettes of it > seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not > public any more. > > So my questions are: > > 1) Is AnnBuilder the right tool for this? > > 2) If not, are there any "right" tools? I don't mind creating the > sqlite database by hand, but how do I create AnnDbBimap objects for > it? > > 3) Are your scripts for building the standard annotation packages > (e.g. org.xx.eg.db) publicly available somewhere? It would be of great > help to see how this is done. > Hi, Gabor. Actually, the AnnBuilder way of building things is deprecated. You will want to use the AnnotationDbi package and refer to the SQLForge vignette. Hope that helps. If you have more specific questions, be sure to include sessionInfo() output. Sean [[alternative HTML version deleted]]
ADD COMMENTlink written 10.6 years ago by Sean Davis21k
Sean, looks great, thanks, G. On Fri, Jan 30, 2009 at 5:22 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > On Fri, Jan 30, 2009 at 11:13 AM, G?bor Cs?rdi <gabor.csardi at="" unil.ch=""> wrote: >> >> Dear All, >> >> I am trying to create an annotation package that contains predicted >> miRNA targets, basically it would be a mapping between Entrez Gene IDs >> and miRNA families, for a couple of organisms, together with some >> additional info or course. >> >> I am trying to make use of the AnnBuilder package, but could not find >> out whether it can do this at all or not. Btw. the vignettes of it >> seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not >> public any more. >> >> So my questions are: >> >> 1) Is AnnBuilder the right tool for this? >> >> 2) If not, are there any "right" tools? I don't mind creating the >> sqlite database by hand, but how do I create AnnDbBimap objects for >> it? >> >> 3) Are your scripts for building the standard annotation packages >> (e.g. org.xx.eg.db) publicly available somewhere? It would be of great >> help to see how this is done. > > Hi, Gabor. Actually, the AnnBuilder way of building things is deprecated. > You will want to use the AnnotationDbi package and refer to the SQLForge > vignette. > > Hope that helps. If you have more specific questions, be sure to include > sessionInfo() output. > > Sean > > > -- Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM
ADD REPLYlink written 10.6 years ago by Gábor Csárdi60
Hi Gabor, I would reccomend that you make a package using the SQLForge vignette as Sean suggested, then use DBI to add your mappings into it as "stand alone" tables so that you can use the createSimpleBimap() to easily make AnnDbBimap objects when your package loads. Please let me know if you need further assistance. Marc G?bor Cs?rdi wrote: > Sean, looks great, thanks, G. > > On Fri, Jan 30, 2009 at 5:22 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Fri, Jan 30, 2009 at 11:13 AM, G?bor Cs?rdi <gabor.csardi at="" unil.ch=""> wrote: >> >>> Dear All, >>> >>> I am trying to create an annotation package that contains predicted >>> miRNA targets, basically it would be a mapping between Entrez Gene IDs >>> and miRNA families, for a couple of organisms, together with some >>> additional info or course. >>> >>> I am trying to make use of the AnnBuilder package, but could not find >>> out whether it can do this at all or not. Btw. the vignettes of it >>> seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not >>> public any more. >>> >>> So my questions are: >>> >>> 1) Is AnnBuilder the right tool for this? >>> >>> 2) If not, are there any "right" tools? I don't mind creating the >>> sqlite database by hand, but how do I create AnnDbBimap objects for >>> it? >>> >>> 3) Are your scripts for building the standard annotation packages >>> (e.g. org.xx.eg.db) publicly available somewhere? It would be of great >>> help to see how this is done. >>> >> Hi, Gabor. Actually, the AnnBuilder way of building things is deprecated. >> You will want to use the AnnotationDbi package and refer to the SQLForge >> vignette. >> >> Hope that helps. If you have more specific questions, be sure to include >> sessionInfo() output. >> >> Sean >> >> >> >> > > > >
ADD REPLYlink written 10.6 years ago by Marc Carlson7.2k
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