make_eupath_organismdbi: Create an organismDbi instance for an eupathdb organism.

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

Create an organismDbi instance for an eupathdb organism.

Description

The primary goal of an organismdbi instance is to provide a series of links between an orgdb, txdb, and other relevant annotation packages (reactome/go/etc). In its current iteration, this function brings together a couple columns from the orgdb, txdb, GO.db, and reactome.db.

Usage

make_eupath_organismdbi(
  entry = NULL,
  eu_version = NULL,
  build_dir = "build",
  installp = TRUE,
  reinstall = FALSE,
  exclude_join = "ENTREZID",
  copy_s3 = FALSE,
  build = TRUE
)

Arguments

entry	A row from the eupathdb metadataframe.
eu_version	Which version of the eupathdb to use for creating this package?
build_dir	Directory in which to build the packages.
installp	Install the resulting package?
reinstall	Overwrite existing data files?
exclude_join	I had a harebrained idea to automatically set up the joins between columns of GO.db/reactome.db/orgdb/txdb objects. This variable is intended to exclude columns with common IDs that might multi-match spuriously – I think in the end I killed the idea though, perhaps this should be removed or resurrected.
copy_s3	Copy the 2bit file into an s3 staging directory for copying to AnnotationHub?

Value

The result of attempting to install the organismDbi package.

Author(s)

Keith Hughitt, modified by atb.

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