[BioC] Problem with intraIDMapper

[Marc Carlson]

Hi Robert,

This method needs to be overhauled and updated now that we have made 
some other improvements to our infrastructure.  A bug has been added to 
my issue tracker for future development and also: thanks for reporting 
this.  It's also good to know that people are using this function.  I 
was actually wondering if maybe I should deprecate it, but now I think 
that maybe I should update it instead.

In the meantime I think you can get much the same functionality by using 
the new select methods.  There is now even a select method for 
inparanoid in the latest development version of AnnotationDbi.  The 
select methods handle missing IDs much more gracefully than the much 
older idConverter function, and they also allow you to recover multiple 
things at once.

In the case you listed below you can already do this by using select 
like so;

library(org.Mm.eg.db)

keys = c("NR_003620","NM_007376")
cols= c("SYMBOL","GENENAME") ## can add however many things you want here.
keytype="REFSEQ"
select(org.Mm.eg.db,keys=keys, cols=cols, keytype=keytype)



   Marc


On 04/16/2012 10:21 AM, Faryabi, Robert (NIH/NCI) [F] wrote:
> Hello,
>
> Here is a problem with idMapper wrappers in AnnotationDbi.
> If you try to map in id that is not in the data base, the function breaks instead of returning a flag that allows handling the situation.
>
>> idConverter("NR_003620", srcSpecies="MUSMU", destSpecies="MUSMU", srcIDType="REFSEQ", destIDType="SYMBOL", keepMultGeneMatches=FALSE, keepMultProtMatches=FALSE, keepMultDestIDMatches = TRUE)
> Error in names(ans)<- unlist(make.name.tree(x, recursive, what.names),  :
>    attempt to set an attribute on NULL
>
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] ggplot2_0.9.0        RSvgDevice_0.6.4.1   Vennerable_2.1
>   [4] xtable_1.7-0         reshape_0.8.4        plyr_1.7.1
>   [7] lattice_0.20-0       RBGL_1.30.1          graph_1.32.0
> [10] venneuler_1.1-0      rJava_0.9-3          pheatmap_0.6.0
> [13] heatmap.plus_1.3     RColorBrewer_1.0-5   Heatplus_2.1.0
> [16] gplots_2.10.1        KernSmooth_2.23-7    caTools_1.12
> [19] bitops_1.0-4.1       gdata_2.8.2          gtools_2.6.2
> [22] org.Mm.eg.db_2.6.4   RSQLite_0.11.1       DBI_0.2-5
> [25] AnnotationDbi_1.16.9 Biobase_2.14.0       rj_1.0.3-7
>
> loaded via a namespace (and not attached):
>   [1] IRanges_1.12.4   MASS_7.3-17      colorspace_1.1-1 dichromat_1.2-4
>   [5] digest_0.5.1     memoise_0.1      munsell_0.3      proto_0.3-9.2
>   [9] reshape2_1.2.1   rj.gd_1.0.3-3    scales_0.2.0     stringr_0.6
> [13] tools_2.14.1
>
> Thanks,
> Robert
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:http://news.gmane.org/gmane.science.biology.informatics.conductor