Dear bioc-devel, I noticed exonsBy is dropping a lot of genes when run on a TxDb object created with makeTxDbFromBiomart (see below). Please also see related post on the Bioconductor support site:
https://support.bioconductor.org/p/101951/#102160 Thanks for your help. Leonard -- > tx <- makeTxDbFromBiomart() > txs_by_gene <- transcriptsBy(tx, "gene") > exs_by_gene <- exonsBy(tx, "gene") > length(txs_by_gene) [1] 63967 > length(exs_by_gene) [1] 36751 > subsetByOverlaps(txs_by_gene, GRanges("8", IRanges(127735434,127741434))) GRangesList object of length 1: $ENSG00000136997 GRanges object with 9 ranges and 2 metadata columns: seqnames ranges strand | tx_id tx_name <Rle> <IRanges> <Rle> | <integer> <character> [1] 8 [127735434, 127740477] + | 101876 ENST00000259523 [2] 8 [127735473, 127735817] + | 101877 ENST00000641252 [3] 8 [127735519, 127738772] + | 101878 ENST00000517291 [4] 8 [127736046, 127736612] + | 101879 ENST00000641036 [5] 8 [127736069, 127741434] + | 101880 ENST00000621592 [6] 8 [127736084, 127741434] + | 101881 ENST00000377970 [7] 8 [127736220, 127741372] + | 101882 ENST00000524013 [8] 8 [127736231, 127738475] + | 101883 ENST00000520751 [9] 8 [127736594, 127740958] + | 101884 ENST00000613283 ------- seqinfo: 555 sequences (1 circular) from an unspecified genome > subsetByOverlaps(exs_by_gene, GRanges("8", IRanges(127735434,127741434))) GRangesList object of length 0: <0 elements> ------- seqinfo: 555 sequences (1 circular) from an unspecified genome > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib 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 utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 Biobase_2.36.2 [4] GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5 [7] S4Vectors_0.14.7 BiocGenerics_0.22.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 XVector_0.16.0 [3] GenomicAlignments_1.12.2 zlibbioc_1.22.0 [5] BiocParallel_1.10.1 bit_1.1-12 [7] lattice_0.20-35 rlang_0.1.2 [9] blob_1.1.0 tools_3.4.1 [11] grid_3.4.1 SummarizedExperiment_1.6.5 [13] DBI_0.7 matrixStats_0.52.2 [15] bit64_0.9-7 digest_0.6.12 [17] tibble_1.3.4 Matrix_1.2-11 [19] GenomeInfoDbData_0.99.0 rtracklayer_1.36.6 [21] bitops_1.0-6 RCurl_1.95-4.8 [23] biomaRt_2.32.1 memoise_1.1.0 [25] RSQLite_2.0 DelayedArray_0.2.7 [27] compiler_3.4.1 Rsamtools_1.28.0 [29] Biostrings_2.44.2 XML_3.98-1.9 [31] pkgconfig_2.0.1 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
