Bioconductor Txdbmaker

txdbmaker

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.8.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: BiocGenerics, S4Vectors, Seqinfo, GenomicRanges, GenomicFeatures
• Imports: httr, rjson, DBI, RSQLite, IRanges, UCSC.utils, GenomeInfoDb, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt
• Install: BiocManager::install("txdbmaker")

When to Use

• Creating TxDb objects from UCSC Genome Browser transcript tables using makeTxDbFromUCSC.
• Retrieving and assembling transcript annotations from BioMart datasets using makeTxDbFromBiomart.
• Extracting transcript information directly from GFF3 or GTF files using makeTxDbFromGFF.
• Saving and loading created TxDb objects to/from SQLite database files using saveDb and loadDb to avoid repeated download times.
• Wrapping a generated database directly into an installable annotation package using makeTxDbPackageFromUCSC or makeTxDbPackageFromBiomart.

When NOT to Use

• For extracting features (like transcripts, exons, and CDS) from an already created TxDb object, use GenomicFeatures instead, which implements the flexible extraction methods.
• For creating TxDb objects from unsupported BioMart datasets (not all BioMart datasets are currently supported by makeTxDbFromBiomart).

Data Requirements

• UCSC: A valid genome build (e.g., "mm9", "hg19") and a supported transcript table (e.g., "knownGene", "refGene").
• BioMart: A supported BioMart dataset name (e.g., "mmusculus_gene_ensembl").
• Files: Local GFF3 or GTF files containing transcript annotations.

Key Parameters

• genome (default): Specifies the genome build (e.g., "mm9") when downloading tables from UCSC.
• tablename (default): Specifies the specific UCSC transcript table to download (e.g., "knownGene").
• dataset (default): Specifies the BioMart dataset to retrieve (e.g., "mmusculus_gene_ensembl").
• circ_seqs (default): A vector specifying which sequences are circular; defaults to the contents of DEFAULT_CIRC_SEQS.
• file (default): The file path used to save or load the SQLite database in saveDb and loadDb.

Best Practices

• Use the supportedUCSCtables utility function to get a list of tables known to work with makeTxDbFromUCSC for your specific genome build.
• Save your annotation objects using saveDb and label them with an appropriate time stamp to facilitate reproducible research and avoid bandwidth costs.
• Use the helper function getChromInfoFromBiomart to check what the different chromosomes are called for a given BioMart source before building the TxDb.

Common Pitfalls

• Re-downloading and assembling databases from UCSC or BioMart every time a script is run. Fix: Use saveDb to save the object locally and loadDb to initialize it from the .sqlite file in future sessions.
• Attempting to serialize a TxDb object using R's base save function. Fix: Use saveDb instead, because TxDb objects are backed by a SQLite database and cannot be serialized normally.

Alternatives

• GenomicFeatures: The companion package where TxDb objects are actually implemented and which provides the methods to extract features from them.
• AnnotationDbi: For querying standard Bioconductor annotation packages (e.g., OrgDb) rather than building transcript-centric databases.

Citations

• Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon and Martin Morgan. Making TxDb Objects. Package txdbmaker.

References

• Homepage: bioconductor.org/packages/txdbmaker
• Vignette: vignette_0_4310e349.txt

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