Question: Creating annotation packages
0
gravatar for Gábor Csárdi
10.5 years ago by
Gábor Csárdi60 wrote:
Marc, thanks, finally I had time for this project. Things went well, mostly, apart from some minor tweaks that I needed. createSimpleBimap() is too simple for me, I have more difficult maps, so I could not use that, but managed to call back to (internal) functions of AnnotationDbi instead. I have two questions. First, I want to define some new classes that extend 'AnnDbBimap', but setClass("miRNAAnnDbBimap", contains="AnnDbBimap") setClass("miRNATargetAnnDbBimap", contains="AnnDbBimap") gives me warnings, because 'AnnObjs' are not exported: Loading required package: DBI Warning message: In .findOrCopyClass(class2, classDef2, where, "subclass") : Class "AnnObj" is defined (with package slot "AnnotationDbi") but no metadata object found to revise subclass information---not exported? Making a copy in package "targetscan.Hs.eg.db" I don't know much about S4, so maybe I am doing something wrong here. Second, for a mapping I have lots of meta data, and it is not clear to me how to define the L2Rchain to get everything right. Right now I am doing this: list(objName="TARGETSFULL", Class="miRNATargetAnnDbBimap", L2Rchain=list( list(tablename="genes", Lcolname="gene_id", Rcolname="_id" ), list(tablename="targets", Lcolname="target", Rattribnames=c( UTR_start="{utr_start}", UTR_end="{utr_end}", MSA_start="{msa_start}", MSA_end="{msa_end}", Seed_match="seed_match.name", PCT="{pct}"), Rattrib_join="LEFT JOIN seed_match ON {seed_match}=seed_match._id LEFT JOIN mirna_family AS _R ON {family}=_R._id", Rcolname="name" ## ), ## list(tablename="mirna_family", ## Lcolname="_id", ## Rcolname="name" ) ) ) which is quite a hack and I cannot use revmap() on this mapping as a result. (Maybe there are other deficiencies I failed to notice so far.) If I use the currently uncommented lines (and remove the second LEFT JOIN and use Rcolname="family", which is the name of the column), then I lose all the attributes listed in Rattribnames. Maybe I am doing something wrong here, I could not find any documentation on how to write the L2Rchains. Or maybe there is some createNonSimpleBimap() function that I should use and I just could not find it. Apart from these, I am happy with the result. Best Regards, Gabor > sessionInfo() R version 2.8.1 (2008-12-22) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] targetscan.Hs.eg.db_5.0-1 RSQLite_0.7-1 [3] DBI_0.2-4 AnnotationDbi_1.5.18 [5] Biobase_2.2.1 > On Fri, Jan 30, 2009 at 7:24 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > 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 >>> >>> >>> >>> >> >> >> >> > > -- Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM
ADD COMMENTlink written 10.5 years ago by Gábor Csárdi60
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