Background: With previous approaches that I would recommend to users for building txdb along the way of making count tables, it was desirable that the GTF release information would *automatically* be passed into the metadata of the rowRanges of the SummarizedExperiment.
for example, in parathyroidSE, using makeTxDbFromBiomart: ... BioMart database version : chr "ENSEMBL GENES 72 (SANGER UK)" BioMart dataset : chr "hsapiens_gene_ensembl" BioMart dataset description : chr "Homo sapiens genes (GRCh37.p11)" or, alternatively, using makeTxDbFromGFF, it would be present in the name of the GTF file: ... Data source: chr "Homo_sapiens.GRCh37.75.gtf" Question: I'm now interested in switching over to using GTF files available through AnnotationHub, and wondering how we can maintain this automatic propagation of metadata. here's some example code: library(GenomicFeatures) library(AnnotationHub) ah <- AnnotationHub() z <- query(ah, c("Ensembl","gtf","Caenorhabditis elegans","release-80")) stopifnot(length(z) == 1) z$title [1] "Caenorhabditis_elegans.WBcel235.80.gtf" gtf <- ah[[names(z)]] metadata(gtf) $AnnotationHubName [1] "AH47045" txdb <- makeTxDbFromGRanges(gtf) metadata(txdb) name 1 Db type 2 Supporting package 3 Genome 4 transcript_nrow 5 exon_nrow 6 cds_nrow 7 Db created by 8 Creation time 9 GenomicFeatures version at creation time 10 RSQLite version at creation time 11 DBSCHEMAVERSION value 1 TxDb 2 GenomicFeatures 3 WBcel235 4 57834 5 173506 6 131562 7 GenomicFeatures package from Bioconductor 8 2015-06-17 09:31:10 +0200 (Wed, 17 Jun 2015) 9 1.21.13 10 1.0.0 11 1.1 sessionInfo() R Under development (unstable) (2015-04-29 r68278) Platform: x86_64-apple-darwin12.5.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices datasets utils [8] methods base other attached packages: [1] AnnotationHub_2.1.26 GenomicFeatures_1.21.13 AnnotationDbi_1.31.16 [4] Biobase_2.29.1 GenomicRanges_1.21.15 GenomeInfoDb_1.5.7 [7] IRanges_2.3.11 S4Vectors_0.7.5 BiocGenerics_0.15.2 [10] testthat_0.10.0 knitr_1.10 BiocInstaller_1.19.6 loaded via a namespace (and not attached): [1] Rcpp_0.11.6 compiler_3.3.0 [3] futile.logger_1.4.1 XVector_0.9.1 [5] bitops_1.0-6 futile.options_1.0.0 [7] tools_3.3.0 zlibbioc_1.15.0 [9] biomaRt_2.25.1 digest_0.6.8 [11] RSQLite_1.0.0 memoise_0.2.1 [13] shiny_0.12.1 DBI_0.3.1 [15] rtracklayer_1.29.10 httr_0.6.1 [17] stringr_1.0.0 Biostrings_2.37.2 [19] R6_2.0.1 XML_3.98-1.2 [21] BiocParallel_1.3.26 lambda.r_1.1.7 [23] magrittr_1.5 Rsamtools_1.21.8 [25] htmltools_0.2.6 GenomicAlignments_1.5.9 [27] SummarizedExperiment_0.1.5 xtable_1.7-4 [29] mime_0.3 interactiveDisplayBase_1.7.0 [31] httpuv_1.3.2 stringi_0.4-1 [33] RCurl_1.95-4.6 crayon_1.3.0 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel