Hi folks, It would be great to have an OrganismDb package for Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and Rattus.norvegicus.
While trying to do this on my own using the Homo.sapiens package as a starting point, I found the most similar looking keys to relate org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and "GENEID" though there's a ".1" tacked to the end "GENEID" which makes it harder to supply the graphInfo object to OrganismDbi:::.loadOrganismDbiPkg: !> key_ <- function(db, key) sort(as.character( + select(db, keys(db, key), key, key)[[key]])) > key_head <- function(db, key) head(key_(db, key)) > key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID") 'select()' returned 1:1 mapping between keys and columns [1] "FBgn0000003.1" "FBgn0000008.1" "FBgn0000014.1" "FBgn0000015.1" [5] "FBgn0000017.1" "FBgn0000018.1" > key_head(org.Dm.eg.db, "ENSEMBL") [1] "FBgn0000008" "FBgn0000014" "FBgn0000015" "FBgn0000017" "FBgn0000018" [6] "FBgn0000022" > In other words, like Rattus.norvegicus, it might be good do add a UCSC "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as good of a candidate (at least without some ugliness)? I was looking at creating a dm6 UCSC "refGene" TxDb. I imagine one would query the UCSC public MySQL server and then do the SQLite conversion. Although the conversion to SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite and I'm having a hard time finding a well supported tool to do it; I don't want to introduce errors or harm reproducibility. What do you use for MySQL to SQLite conversion? Or would it be more sensible for you benevolent dictators to generate the package(s)? Pariksheet --- Pariksheet Nanda PhD Candidate in Genetics and Genomics System Administrator, Storrs HPC Cluster University of Connecticut --- > sessionInfo() R Under development (unstable) (2016-11-13 r71655) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] Rattus.norvegicus_1.3.1 [2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0 [3] org.Rn.eg.db_3.4.0 [4] Mus.musculus_1.3.1 [5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [6] org.Mm.eg.db_3.4.0 [7] Homo.sapiens_1.3.1 [8] GO.db_3.4.0 [9] OrganismDbi_1.17.1 [10] org.Hs.eg.db_3.4.0 [11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [12] org.Dm.eg.db_3.4.0 [13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0 [14] GenomicFeatures_1.27.2 [15] AnnotationDbi_1.37.0 [16] Biobase_2.35.0 [17] GenomicRanges_1.27.6 [18] GenomeInfoDb_1.11.4 [19] IRanges_2.9.8 [20] S4Vectors_0.13.2 [21] BiocGenerics_0.21.0 [22] BiocInstaller_1.25.2 loaded via a namespace (and not attached): [1] compiler_3.4.0 XVector_0.15.0 [3] bitops_1.0-6 tools_3.4.0 [5] zlibbioc_1.21.0 biomaRt_2.31.1 [7] RSQLite_1.0.0 lattice_0.20-34 [9] Matrix_1.2-7.1 graph_1.53.0 [11] DBI_0.5-1 rtracklayer_1.35.1 [13] Biostrings_2.43.0 grid_3.4.0 [15] XML_3.98-1.5 RBGL_1.51.0 [17] BiocParallel_1.9.1 Rsamtools_1.27.2 [19] GenomicAlignments_1.11.1 SummarizedExperiment_1.5.3 [21] RCurl_1.95-4.8 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel