getTximetaBFC: Get or set the directory of the BiocFileCache used by tximeta

In tximeta: Transcript Quantification Import with Automatic Metadata

Description

Running getTximetaBFC will report the saved directory, if it has been determined, or will return NULL. Running setTximetaBFC will ask the user to specify a BiocFileCache directory for accessing and saving TxDb sqlite files. Note that tximeta's BiocFileCache can be set by the environmental variable TXIMETA_HUB_CACHE, which will reset the cache location.

Usage

getTximetaBFC()

setTximetaBFC(dir, quiet = FALSE)

Arguments

dir	the location for tximeta's BiocFileCache. can be missing in which case the function will call file.choose for choosing location interactively
quiet	whether to suppress feedback message

Value

the directory of the BiocFileCache used by tximeta (or nothing, in the case of setTximetaBFC)

Examples

# getting the BiocFileCache used by tximeta
# (may not be set, which uses BiocFileCache default or temp directory)
getTximetaBFC()

# don't want to actually change user settings so this is not run:
# setTximetaBFC()

tximeta documentation built on April 13, 2021, 6:01 p.m.