jorainer
commented
10 months ago The example code works because the full genomic region is within the transcript (i.e. one of its exons): see also the respective region in the Ensembl genome browser here.
Your region defines a large genomic region that contains a full transcript and also downstream sequence (see here). The functions to map between genomic and transcript or protein coordinates (genomeToTranscript genomeToProtein) can only map genomic regions that are within an exon of a transcript to the respective coordinates within that transcript (i.e. convert between genomic coordinates and transcript-relative coordinates).
So, these functions can only be used to convert between these coordinate systems. Genomic coordinates that do not code for an exon of a transcript can not be converted to transcript coordinates.
If instead you were looking for a way to identify transcripts that are located in a certain genomic region:
> gnm <- GRanges("6:88109864-88166347")
> transcripts(edb, filter = GRangesFilter(gnm))
GRanges object with 7 ranges and 11 metadata columns:
seqnames ranges strand | tx_id
<Rle> <IRanges> <Rle> | <character>
ENST00000362094 6 88139864-88145274 - | ENST00000362094
ENST00000468898 6 88139864-88145274 - | ENST00000468898
... ... ... ... . ...
ENST00000369501 6 88139864-88166347 - | ENST00000369501
ENST00000551417 6 88139864-88166347 - | ENST00000551417
tx_biotype tx_cds_seq_start tx_cds_seq_end
<character> <integer> <integer>
ENST00000362094 protein_coding 88144997 88145274
ENST00000468898 protein_coding 88143856 88145274
... ... ... ...
ENST00000369501 protein_coding 88143856 88145274
ENST00000551417 protein_coding 88143856 88145274
gene_id tx_support_level tx_id_version gc_content
<character> <integer> <character> <numeric>
ENST00000362094 ENSG00000118432 1 ENST00000362094.6 40.5797
ENST00000468898 ENSG00000118432 1 ENST00000468898.2 40.7568
... ... ... ... ...
ENST00000369501 ENSG00000118432 1 ENST00000369501.3 43.8611
ENST00000551417 ENSG00000118432 5 ENST00000551417.2 44.0806
tx_external_name tx_is_canonical tx_name
<character> <integer> <character>
ENST00000362094 CNR1-201 0 ENST00000362094
ENST00000468898 CNR1-205 0 ENST00000468898
... ... ... ...
ENST00000369501 CNR1-203 1 ENST00000369501
ENST00000551417 CNR1-207 0 ENST00000551417
-------
seqinfo: 1 sequence from GRCh38 genome
cjagla
Hi, I'm trying to use
genomeToTranscript()to convert exon coordinates from genomic to transcript-based for specific human genes. I can't get any examples of genomic coordinates to work other than the one you've provided in the function manual, including a very large chunk of chromosome 6 that should definitely contain many genes or the entirety of chromosome 19. Can you please assist?`> a[["9606"]] EnsDb for Ensembl: |Backend: SQLite |Db type: EnsDb |Type of Gene ID: Ensembl Gene ID |Supporting package: ensembldb |Db created by: ensembldb package from Bioconductor |script_version: 0.3.10 |Creation time: Thu Feb 16 12:36:05 2023 |ensembl_version: 109 |ensembl_host: localhost |Organism: Homo sapiens |taxonomy_id: 9606 |genome_build: GRCh38 |DBSCHEMAVERSION: 2.2 |common_name: human |species: homo_sapiens | No. of genes: 70623. | No. of transcripts: 276218. |Protein data available.
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.21.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] ensembldb_2.22.0 AnnotationFilter_1.22.0 GenomicFeatures_1.50.4 AnnotationDbi_1.60.2 Biobase_2.58.0 GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2 AnnotationHub_3.6.0 BiocFileCache_2.6.1 dbplyr_2.3.3
[13] BiocGenerics_0.44.0 stringr_1.5.0 dplyr_1.1.2 jsonlite_1.8.7 readr_2.1.4 tidyr_1.3.0
[19] xml2_1.3.5 biomaRt_2.54.1
loaded via a namespace (and not attached): [1] ProtGenerics_1.30.0 bitops_1.0-7 matrixStats_1.0.0 bit64_4.0.5 filelock_1.0.2
[6] progress_1.2.2 httr_1.4.7 tools_4.2.2 utf8_1.2.3 R6_2.5.1
[11] DBI_1.1.3 lazyeval_0.2.2 withr_2.5.0 tidyselect_1.2.0 prettyunits_1.1.1
[16] bit_4.0.5 curl_5.0.2 compiler_4.2.2 cli_3.6.1 DelayedArray_0.24.0
[21] rtracklayer_1.58.0 rappdirs_0.3.3 digest_0.6.33 Rsamtools_2.14.0 XVector_0.38.0
[26] pkgconfig_2.0.3 htmltools_0.5.6 MatrixGenerics_1.10.0 fastmap_1.1.1 rlang_1.1.1
[31] RSQLite_2.3.1 shiny_1.7.5 BiocIO_1.8.0 generics_0.1.3 BiocParallel_1.32.6
[36] RCurl_1.98-1.12 magrittr_2.0.3 GenomeInfoDbData_1.2.9 Matrix_1.5-1 Rcpp_1.0.11
[41] fansi_1.0.4 lifecycle_1.0.3 stringi_1.7.12 yaml_2.3.7 SummarizedExperiment_1.28.0
[46] zlibbioc_1.44.0 grid_4.2.2 blob_1.2.4 parallel_4.2.2 promises_1.2.1
[51] crayon_1.5.2 lattice_0.20-45 Biostrings_2.66.0 hms_1.1.3 KEGGREST_1.38.0
[56] pillar_1.9.0 rjson_0.2.21 codetools_0.2-18 XML_3.99-0.14 glue_1.6.2
[61] BiocVersion_3.16.0 renv_1.0.2 BiocManager_1.30.22 png_0.1-8 vctrs_0.6.3
[66] tzdb_0.4.0 httpuv_1.6.11 purrr_1.0.2 cachem_1.0.8 mime_0.12
[71] xtable_1.8-4 restfulr_0.0.15 later_1.3.1 tibble_3.2.1 GenomicAlignments_1.34.1
[76] memoise_2.0.1 ellipsis_0.3.2 interactiveDisplayBase_1.36.0`