set_go_data: GAPGOM - set_go_data()

In Berghopper/GAPGOM: GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Description

Sets GO data like GOSemSim (this function purely makes choosing datasets a little easier and prints available keytypes if specified incorrectly.)

Usage

set_go_data(organism, ontology, computeIC = TRUE, keytype = "ENTREZID")

Arguments

organism	where to be scanned genes reside in, this option is neccesary to select the correct GO DAG. Options are based on the org.db bioconductor package; http://www.bioconductor.org/packages/release/BiocViews.html#___OrgDb Following options are available: "fly", "mouse", "rat", "yeast", "zebrafish", "worm", "arabidopsis", "ecolik12", "bovine", "canine", "anopheles", "ecsakai", "chicken", "chimp", "malaria", "rhesus", "pig", "xenopus". Fantom5 data only has "human" and "mouse" available depending on the dataset.
ontology	desired ontology to use for prediction. One of three; "BP" (Biological process), "MF" (Molecular function) or "CC" (Cellular Component). Cellular Component is not included with the package's standard data and will thus yield no results.
computeIC	whether to compute Information Content.
keytype	keytype used in querying of godata

Value

return godata as from GoSemSim

Notes

Internal function used in multiple functions of topoICSim.

Examples

# set go data for human, MF ontology.
go_data <- GAPGOM::set_go_data("human", "MF")

Berghopper/GAPGOM documentation built on July 2, 2020, 11:57 p.m.