ToastGoSlim: Assign Go_Slim IDs to BUSCO IDs

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

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, [e-mail]

James Thomas Howard, [e-mail]

Jeffrey A Yoder, [e-mail]

Alex Dornburg, [e-mail]

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 Dec. 19, 2024, 12:47 a.m.