suppressPackageStartupMessages({
library(txdbmaker)
})
gff_file <- system.file("extdata", "GFF3_files", "a.gff3", package="txdbmaker")
txdb <- makeTxDbFromGFF(gff_file, format="gff3")
txdb
#> TxDb object:
#> # Db type: TxDb
#> # Supporting package: GenomicFeatures
#> # Data source: /Users/runner/work/_temp/Library/txdbmaker/extdata/GFF3_files/a.gff3
#> # Organism: NA
#> # Taxonomy ID: NA
#> # miRBase build ID: NA
#> # Genome: NA
#> # Nb of transcripts: 488
#> # Db created by: txdbmaker package from Bioconductor
#> # Creation time: 2025-02-17 15:47:55 +0000 (Mon, 17 Feb 2025)
#> # txdbmaker version at creation time: 1.3.1
#> # RSQLite version at creation time: 2.3.9
#> # DBSCHEMAVERSION: 1.2How to load a gene model from a GFF or GTF file
2025-02-17
A gene model is essentially a set of annotations that describes the genomic locations of the known genes, transcripts, exons, and CDS, for a given organism. The standardized file format to hold gene models is a GFF or GTF. In Bioconductor, gene model information is typically represented as a TxDb object but also sometimes as a GRanges or GRangesList object. We can use the makeTxDbFromGFF() function from the txdbmaker package to import a GFF or GTF file as a TxDb object.
Bioconductor packages used in this document
How to load a gene model from a GFF or GTF file
We will use a small .gff3 file provided by the txdbmaker package.
See ?makeTxDbFromGFF in the txdbmaker package for more information.
Extract the exon coordinates grouped by gene from this gene model:
exonsBy(txdb, by="gene")
#> GRangesList object of length 488:
#> $Solyc00g005000.2
#> GRanges object with 2 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id exon_name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] SL2.40ch00 16437-17275 + | 1 Solyc00g005000.2.1.1
#> [2] SL2.40ch00 17336-18189 + | 2 Solyc00g005000.2.1.2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $Solyc00g005020.1
#> GRanges object with 3 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id exon_name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] SL2.40ch00 68062-68211 + | 3 Solyc00g005020.1.1.1
#> [2] SL2.40ch00 68344-68568 + | 4 Solyc00g005020.1.1.2
#> [3] SL2.40ch00 68654-68764 + | 5 Solyc00g005020.1.1.3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $Solyc00g005040.2
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id exon_name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] SL2.40ch00 550920-550945 + | 6 Solyc00g005040.2.1.1
#> [2] SL2.40ch00 551034-551132 + | 7 Solyc00g005040.2.1.2
#> [3] SL2.40ch00 551218-551250 + | 8 Solyc00g005040.2.1.3
#> [4] SL2.40ch00 551343-551576 + | 9 Solyc00g005040.2.1.4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> ...
#> <485 more elements>Session info
Click to display session info
sessionInfo()
#> R Under development (unstable) (2025-02-15 r87725)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sonoma 14.7.2
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: UTC
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] txdbmaker_1.3.1 GenomicFeatures_1.59.1 AnnotationDbi_1.69.0
#> [4] Biobase_2.67.0 GenomicRanges_1.59.1 GenomeInfoDb_1.43.4
#> [7] IRanges_2.41.3 S4Vectors_0.45.4 BiocGenerics_0.53.6
#> [10] generics_0.1.3 BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] KEGGREST_1.47.0 SummarizedExperiment_1.37.0
#> [3] httr2_1.1.0 rjson_0.2.23
#> [5] xfun_0.50 lattice_0.22-6
#> [7] vctrs_0.6.5 tools_4.5.0
#> [9] bitops_1.0-9 curl_6.2.0
#> [11] parallel_4.5.0 tibble_3.2.1
#> [13] RSQLite_2.3.9 blob_1.2.4
#> [15] pkgconfig_2.0.3 Matrix_1.7-2
#> [17] dbplyr_2.5.0 lifecycle_1.0.4
#> [19] GenomeInfoDbData_1.2.13 stringr_1.5.1
#> [21] compiler_4.5.0 Rsamtools_2.23.1
#> [23] Biostrings_2.75.3 progress_1.2.3
#> [25] codetools_0.2-20 htmltools_0.5.8.1
#> [27] RCurl_1.98-1.16 yaml_2.3.10
#> [29] pillar_1.10.1 crayon_1.5.3
#> [31] BiocParallel_1.41.0 cachem_1.1.0
#> [33] DelayedArray_0.33.6 abind_1.4-8
#> [35] tidyselect_1.2.1 digest_0.6.37
#> [37] stringi_1.8.4 dplyr_1.1.4
#> [39] restfulr_0.0.15 biomaRt_2.63.1
#> [41] fastmap_1.2.0 grid_4.5.0
#> [43] cli_3.6.4 SparseArray_1.7.5
#> [45] magrittr_2.0.3 S4Arrays_1.7.3
#> [47] XML_3.99-0.18 filelock_1.0.3
#> [49] rappdirs_0.3.3 prettyunits_1.2.0
#> [51] UCSC.utils_1.3.1 bit64_4.6.0-1
#> [53] rmarkdown_2.29 XVector_0.47.2
#> [55] httr_1.4.7 matrixStats_1.5.0
#> [57] bit_4.5.0.1 png_0.1-8
#> [59] hms_1.1.3 memoise_2.0.1
#> [61] evaluate_1.0.3 knitr_1.49
#> [63] BiocIO_1.17.1 BiocFileCache_2.15.1
#> [65] rtracklayer_1.67.0 rlang_1.1.5
#> [67] glue_1.8.0 DBI_1.2.3
#> [69] xml2_1.3.6 BiocManager_1.30.25
#> [71] jsonlite_1.8.9 R6_2.6.1
#> [73] MatrixGenerics_1.19.1 GenomicAlignments_1.43.0