Hi guys, Thanks for your feedbacks. Indeed I put GENEID because it is used in the txdb database.
> library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > columns(txdb) [1] "CDSID" "CDSNAME" "CDSCHROM" "CDSSTRAND" "CDSSTART" [6] "CDSEND" "EXONID" "EXONNAME" "EXONCHROM" "EXONSTRAND" [11] "EXONSTART" "EXONEND" "GENEID" "TXID" "EXONRANK" [16] "TXNAME" "TXCHROM" "TXSTRAND" "TXSTART" "TXEND" I will move to ENTREZID which is much faster ! I'm glad It could help Nicolas ________________________________________ De : bioc-devel-boun...@r-project.org [bioc-devel-boun...@r-project.org] de la part de Marc Carlson [mcarl...@fhcrc.org] Date d'envoi : mercredi 12 mars 2014 20:18 À : bioc-devel@r-project.org Objet : Re: [Bioc-devel] AnnotationDbi and select function Thanks Nicolaus! That's a good bug. I will work on a fix. The reason why James work-around here functions is because the number of databases that it has to query is fewer by one. It is also faster for this reason. So when you say GENEID you mean the ids used in the associated txdb database which means that these have to be checked against that DB (and anything related to it extracted) and then merged with the results of the symbol information by joining on the foreign key for these two DBs. So thats actually much more complex than just extracting all the same data from just the org package even though the end result (in this case) is the same. The bug is probably happening in the associated merge step. Marc On 03/12/2014 10:06 AM, James W. MacDonald wrote: > 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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel