Make tx2gene data.frame from a TxDb object

Make tx2gene data.frame from a TxDb object and an org.*.eg.db annotation package.

Usage

makeTx2geneFromTxdb(txdb, ann_lib, verbose = FALSE, ...)

Arguments

txdb

TxDb object, such as those provided by Bioconductor packages like TxDb.Mmusculus.UCSC.mm10.knownGene or TxDb.Hsapiens.UCSC.hg38.knownGene.

ann_lib

character string naming an installed Bioconductor organism annotation package (e.g. "org.Mm.eg.db" for mouse or "org.Hs.eg.db" for human). Must match the organism used in txdb. No validation of organism concordance is performed.

verbose

logical whether to print verbose output during processing.

...

additional arguments are ignored.

Value

data.frame with colnames "transcript_id", "gene_id", "gene_name". gene_id contains the ENTREZID values from the TxDb, and gene_name contains the resolved gene SYMBOL.

Details

This function converts a Bioconductor TxDb annotation package (e.g. TxDb.Mmusculus.UCSC.mm10.knownGene) into the three-column data.frame expected by splicejam: transcript_id, gene_id, gene_name.

Gene IDs in UCSC-style TxDb objects are NCBI Entrez IDs (ENTREZID). These are mapped to gene symbols (SYMBOL) using genejam::freshenGenes() with the supplied ann_lib. When an ENTREZID cannot be resolved to a SYMBOL, the original ENTREZID is retained as the gene_name (controlled by empty_rule="original" in freshenGenes()).

Exception: Some TxDb packages with suffix 'ensDb' use EnsEMBL gene identifier, in the form 'ENSG00000001' or 'ENSMUSG00000001'. In this case, genejam::freshenGenes() will be used to query by the 'ENSEMBL2EG' annotation data, and will fallback to use the EnsEMBL gene_id when not found.

See also

makeTx2geneFromGtf() for the GTF-based equivalent, splicejamDataFromTxDb() for the higher-level workflow that calls this function.

Other GTF functions: describeGtfAttrNames(), getGtfAttrs(), makeTx2geneFromGtf(), readGtf()