bioconductor-genomicfeatures

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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