View source: R/ToastGoSlim_testingFunction.R View source: R/ToastGoSlim.R
ToastGoSlim | R Documentation |
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
ToastGoSlim(orthogroup_info, obo, perspective = "BP")
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) |
Dustin J Wcisel, djwcisel@ncsu.edu
James Thomas Howard, jthowar3@ncsu.edu
Jeffrey A Yoder, jayoder@ncsu.edu
Alex Dornburg, dornburgalex@gmail.com
BP <- ToastGoSlim(orthogroup_info = "path/to/orthoDB/info/*orthogroup_info.txt.gz", obo = "path/to/goslim_agr.obo", perspective = "BP")
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