dot-generate_translation_df: GAPGOM internal - .generate_translation_df()

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

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().

GAPGOM documentation built on Nov. 8, 2020, 8:08 p.m.