set_go_data {GAPGOM} | R Documentation

## GAPGOM - set_go_data()

### 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")

[Package GAPGOM version 1.4.0 Index]