.generate_translation_df {GAPGOM} | R Documentation

## GAPGOM internal - .generate_translation_df()

### Description

This function is an internal function and should not be called by the user.

### Usage

    .generate_translation_df(expression_set, organism, ontology, keytype,
      verbose = FALSE, go_data = NULL)

### Arguments

`expression_set` | ExpressionSet object –> see Biobase package.
`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.
`keytype` | keytype used in querying of godata/columnnames
`verbose` | set to true for more informative/elaborate output.

### Details

Generates a translation df specific for ExpressionSets, this is then used for looking up ids and their respective GOIDS.

### Value

return the translation dataframe containing conversion from general ids to entrez/ensembl ids (and others) and goids.

### Notes

Internal function used in expression_prediction_function().

[Package GAPGOM version 1.4.0 Index]