load_eupath_go: Shortcut for loading annotation data from a eupathdb-based...

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

Shortcut for loading annotation data from a eupathdb-based orgdb.

Description

Every time I go to load the annotation data from an orgdb for a parasite, it takes me an annoyingly long time to get the darn flags right. As a result I wrote this to shortcut that process. Ideally, one should only need to pass it a species name and get out a nice big table of annotation data.

Usage

load_eupath_go(
  query,
  webservice = "tritrypdb",
  eu_version = NULL,
  wanted_fields = NULL,
  gene_ids = NULL,
  columns = c("go", "evidence")
)

Arguments

query	String containing a unique portion of the desired species.
webservice	Which eupath webservice is desired?
eu_version	Gather data from a specific eupathdb version?
wanted_fields	If not provided, this will gather all columns starting with 'annot'.
gene_ids	Set of gene IDs to download GO data.
columns	Wanted GO columns.

Value

Big huge data frame of annotation data.

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