make_eupath_txdb: Generate an EuPathDB organism TxDb package.

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Generate an EuPathDB organism TxDb package.

Description

This will hopefully create a txdb package and granges savefile for a single species in the eupathdb. This depends pretty much entirely on the successful download of a gff file from the eupathdb.

Usage

make_eupath_txdb(
  entry = NULL,
  eu_version = NULL,
  reinstall = FALSE,
  install = TRUE,
  copy_s3 = FALSE,
  verbose = FALSE,
  build_dir = "build",
  build = TRUE
)

Arguments

entry	One row from the organism metadata.
eu_version	Which version of the eupathdb to use for creating this package?
reinstall	Overwrite an existing installed package?
install	Install the resulting package?
copy_s3	Copy the 2bit file into an s3 staging directory for copying to AnnotationHub?
build_dir	Base directory for building the package.

Value

TxDb instance name.

Author(s)

Keith Hughitt with significant modifications by atb.

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.