Set default TxDb for downstream annotation helpers

Record a preferred TxDb to use when functions such as annotateWindows() are called without an explicit TxDb.

setMesaTxDb(TxDb)

Arguments

TxDb

character(1), TxDb object, or NULL. Either the name of an installed TxDb package (e.g., "TxDb.Hsapiens.UCSC.hg38.knownGene"), the TxDb object itself, or NULL to clear the setting. If a string is supplied, the package must be installed. Default: none (must be supplied).

Value

Invisibly returns TRUE on success.

Details

This sets the session option options(mesa_TxDb = TxDb). When a string is stored, helpers like annotateWindows() will load the TxDb object on demand (e.g., "TxDb.Hsapiens.UCSC.hg38.knownGene"). Use setMesaGenome() and setMesaAnnoDb() to configure complementary defaults for genome and OrgDb.

See also

annotateWindows(), setMesaGenome(), setMesaAnnoDb(), ChIPseeker::annotatePeak()

Examples

# Set default TxDb for human (GRCh38/hg38)
setMesaTxDb("TxDb.Hsapiens.UCSC.hg38.knownGene")
getOption("mesa_TxDb")
#> [1] "TxDb.Hsapiens.UCSC.hg38.knownGene"

# Clear the default TxDb
setMesaTxDb(NULL)
getOption("mesa_TxDb")
#> NULL

# (Alternatively) you can store the object itself if already loaded:
# setMesaTxDb(
#   TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
# )