| name | bioconductor-genomicfeatures |
| description | Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a |
| when_to_use | Use when: Extract genomic coordinates for exons, transcripts, or coding sequences as GRanges objects using transcripts, exons, or cds.; Group genomic features by gene or transcript into a GRangesList using transcriptsBy or exonsBy.; Retrieve actual sequence data by pairing a TxDb with a BSgenome package and using extractTranscriptSeqs.. Not for: For extracting actual sequence data without a BSgenome package (use BSgenome directly instead because GenomicFeatures only stores coordinates).; For finding overlaps between alignments and features without first extracting the features (use findOverl |
| user-invocable | false |
GenomicFeatures
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.64.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: BiocGenerics, S4Vectors, IRanges, Seqinfo, GenomicRanges, AnnotationDbi
- Imports: DBI, XVector, Biostrings, rtracklayer
- Install:
BiocManager::install("GenomicFeatures")
When to Use
- Extract genomic coordinates for exons, transcripts, or coding sequences as
GRanges objects using transcripts, exons, or cds.
- Group genomic features by gene or transcript into a
GRangesList using transcriptsBy or exonsBy.
- Retrieve actual sequence data by pairing a
TxDb with a BSgenome package and using extractTranscriptSeqs.
When NOT to Use
- For extracting actual sequence data without a
BSgenome package (use BSgenome directly instead because GenomicFeatures only stores coordinates).
- For finding overlaps between alignments and features without first extracting the features (use
findOverlaps on the extracted GRangesList instead).
Data Requirements
- Requires a
TxDb object (loaded via loadDb or an annotation package like TxDb.Hsapiens.UCSC.hg19.knownGene).
- Sequence extraction requires an appropriate
BSgenome package (e.g., BSgenome.Hsapiens.UCSC.hg19).
Key Parameters
- keys (default): A vector of identifiers to look up when using
select.
- columns (default): The columns to retrieve when using
select.
- keytype (default): The type of key being passed to
select.
- filter (default): A list (e.g.,
tx_chrom, tx_strand) to subset results in transcripts.
- upstream (default): Number of bases upstream from the transcription start site for
promoters.
- downstream (default): Number of bases downstream from the transcription start site for
promoters.
- by (default): The feature to group by (e.g., "gene", "tx") in
transcriptsBy or exonsBy.
- use.names (default): Logical to retain sequence names in
extractTranscriptSeqs.
Best Practices
- Check active chromosomes using
seqlevels before extracting features to limit the data returned.
- Use
select to map between different identifiers (e.g., TXNAME to GENEID) within the TxDb object.
- Group features into a
GRangesList (e.g., using exonsBy) before using findOverlaps to contextualize high-throughput sequencing alignments.
Common Pitfalls
- Extracting sequences for all transcribed regions instead of just coding regions. Fix: Use
cdsBy to subset coding regions before calling extractTranscriptSeqs.
- Translating non-coding sequences resulting in meaningless translations. Fix: Ensure you extract sequences using
cdsBy before passing them to translate.
- Forgetting which chromosomes are active after filtering. Fix: Use
seqlevels0 to reset to the original chromosomes stored in the database.
Alternatives
txdbmaker: For making TxDb objects from genomic annotations (UCSC, Ensembl, GFF) rather than querying existing ones.BSgenome: For working directly with full genome sequences rather than transcript-specific metadata.GenomicRanges: For general manipulation of GRanges objects rather than extracting them from a database.
Citations
- Carlson M, Aboyoun P, Pagès H, Falcon S, Morgan M (2026). "Obtaining and Utilizing TxDb Objects." Bioconductor Vignette.
References
- Homepage: bioconductor.org/packages/GenomicFeatures
- Vignette: vignette_0_d47eae8b.txt
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