make_eupath_orgdb: Create an orgdb SQLite database from the tables in eupathdb.
In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

make_eupath_orgdb

R Documentation

Create an orgdb SQLite database from the tables in eupathdb.

Description

This function has passed through multiple iterations as the preferred method(s) for accessing data in the eupathdb has changed. It currently uses my empirically defined set of queries against the eupathdb webservices. As a result, I have made some admittedly bizarre choices when creating the queries. Check through eupath_webservices.r for some amusing examples of how I have gotten around the idiosyncrasies in the eupathdb. Final note, I confirmed with Cristina that it is not possible to acquire data specific to a given version of the eupathdb.

Usage

make_eupath_orgdb(
  entry,
  install = TRUE,
  reinstall = FALSE,
  overwrite = FALSE,
  verbose = FALSE,
  copy_s3 = FALSE,
  godb_source = NULL,
  split = 13,
  build_dir = "build",
  build = TRUE
)

Arguments

`entry`	If not provided, then species will get this, it contains all the information.
`install`	Install the resulting package?
`reinstall`	Re-install an already existing orgdb?
`overwrite`	Overwrite a partial installation?
`verbose`	talky talky
`copy_s3`	Copy the 2bit file into an s3 staging directory for copying to AnnotationHub?
`godb_source`	Which table to use for the putative union of the GO tables.
`build_dir`	Where to put all the various temporary files.