ToastGoSlim: Assign Go_Slim IDs to BUSCO IDs

View source: R/ToastGoSlim_testingFunction.R View source: R/ToastGoSlim.R

ToastGoSlimR Documentation

Assign Go_Slim IDs to BUSCO IDs

Description

this function takes the Gene Ontology information contained in the orthoDB and generalizes it into as as few GO terms as possible given three perspectives: Molecular function, Biological Process and Cellular Component, each returned as a dataframe

Usage

ToastGoSlim(orthogroup_info, obo, perspective = "BP")

Arguments

orthogroup_info

assing the uncompressed ontology file found in orthoDB/info/*orthogroup_info.txt.gz

obo

download desired ontology information (.obo file) from http://geneontology.org/docs/download-ontology/#go_obo_and_owl these are consistently updated so make sure to grab the newest we recommend the GO slim AGR subset (goslim_agr.obo) which can be obtained using the command wget http://current.geneontology.org/ontology/subsets/goslim_agr.obo

perspective

options are BP(biological process), MF(Molecular function), or CC(cellular component)

Author(s)

Dustin J Wcisel, djwcisel@ncsu.edu

James Thomas Howard, jthowar3@ncsu.edu

Jeffrey A Yoder, jayoder@ncsu.edu

Alex Dornburg, dornburgalex@gmail.com

Examples

BP <- ToastGoSlim(orthogroup_info = "path/to/orthoDB/info/*orthogroup_info.txt.gz", obo = "path/to/goslim_agr.obo", perspective = "BP")

carolinafishes/toast documentation built on June 28, 2023, 8:10 p.m.