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