[Bioc-devel] AnnotationDbi and select function

[James W. MacDonald]

Hi Nicolas,

On 3/12/2014 12:39 PM, Servant Nicolas wrote:
> Dear all,
>
> I have an error using the select function from the AnnotationDbi package.
> I try to convert some geneID into Symbol, but for some strange reasons it crashed.
>
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> isActiveSeq(txdb)[seqlevels(txdb)] <- FALSE
> isActiveSeq(txdb)[c("chr16","chr1")] <- TRUE
> geneGR <- exonsBy(txdb, "gene")
> library(Homo.sapiens)
> symbol <- select(Homo.sapiens, keys = names(geneGR), keytype = "GENEID", columns = "SYMBOL")
> Erreur dans head(select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype = "GENEID",  :
>    erreur d'évaluation de l'argument 'x' lors de la sélection d'une méthode pour la fonction 'head' : Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
>
>> length(geneGR)
> [1] 3269
> ## The first 1K work
>> symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1000], keytype = "GENEID", columns = "SYMBOL")
> ## The 1K+1 does not !
>> symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype = "GENEID", columns = "SYMBOL")
> Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
>    nombre de dimensions incorrect
>
> It looks like I cannot convert more than 1K elements ?? Any reason for that ?
> Thank you very much
> Nicolas

Not sure what 'GENEID' is in this context - it appears to be Entrez 
Gene. But anyway, if you use "ENTREZID" instead, it works fine:

 > symbol <- select(Homo.sapiens, names(geneGR), "SYMBOL", "ENTREZID")
 > symbol <- select(Homo.sapiens, names(geneGR), "GENEID", "ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
   incorrect number of dimensions
 > symbol <- select(Homo.sapiens, names(geneGR)[1:1000], "GENEID", 
"ENTREZID")
 > symbol <- select(Homo.sapiens, names(geneGR)[1:1001], "GENEID", 
"ENTREZID")
Error in res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
   incorrect number of dimensions

Best,

Jim



>
>> sessionInfo()
> R Under development (unstable) (2014-03-05 r65125)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
>   [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
>   [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] Homo.sapiens_1.1.2
>   [2] org.Hs.eg.db_2.10.1
>   [3] GO.db_2.10.1
>   [4] RSQLite_0.11.4
>   [5] DBI_0.2-7
>   [6] OrganismDbi_1.5.3
>   [7] XVector_0.3.7
>   [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
>   [9] GenomicFeatures_1.15.9
> [10] AnnotationDbi_1.25.14
> [11] GenomeInfoDb_0.99.17
> [12] Biobase_2.23.6
> [13] GenomicRanges_1.15.32
> [14] IRanges_1.21.32
> [15] BiocGenerics_0.9.3
> [16] RColorBrewer_1.0-5
> [17] reshape2_1.2.2
> [18] reshape_0.8.4
> [19] plyr_1.8.1
> [20] ggplot2_0.9.3.1
> [21] Matrix_1.1-2-2
>
> loaded via a namespace (and not attached):
>   [1] BatchJobs_1.2             BBmisc_1.5
>   [3] BiocParallel_0.5.16       biomaRt_2.19.3
>   [5] Biostrings_2.31.14        bitops_1.0-6
>   [7] brew_1.0-6                BSgenome_1.31.12
>   [9] codetools_0.2-8           colorspace_1.2-4
> [11] dichromat_2.0-0           digest_0.6.4
> [13] fail_1.2                  foreach_1.4.1
> [15] GenomicAlignments_0.99.29 graph_1.41.3
> [17] grid_3.1.0                gtable_0.1.2
> [19] iterators_1.0.6           labeling_0.2
> [21] lattice_0.20-27           MASS_7.3-29
> [23] munsell_0.4.2             proto_0.3-10
> [25] RBGL_1.39.2               Rcpp_0.11.0
> [27] RCurl_1.95-4.1            Rsamtools_1.15.32
> [29] rtracklayer_1.23.15       scales_0.2.3
> [31] sendmailR_1.1-2           stats4_3.1.0
> [33] stringr_0.6.2             tools_3.1.0
> [35] XML_3.98-1.1              zlibbioc_1.9.0
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099