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 > 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]]
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