[BioC] Problem with intraIDMapper

Faryabi, Robert (NIH/NCI) [F] Babak.Faryabi at nih.gov
Mon Apr 16 19:21:49 CEST 2012


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)

[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


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