Creating annotation packages
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@gabor-csardi-3111
Last seen 8.2 years ago
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 the vignettes of it seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not public any more.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 miRNA Annotation AnnBuilder • 763 views
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@sean-davis-490
Last seen 3 months ago
United States
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 seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not 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]]
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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
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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 >> >> >> >> > > > >
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