convert_gsc_ids: Use AnnotationDbi to translate geneIDs from type x to type y.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Use AnnotationDbi to translate geneIDs from type x to type y.

Description

This is intended to convert all the IDs in a geneSet from one ID type to another and giving back the geneSet with the new IDs. FIXME: This should use convert_ids() to simplify itself

Usage

convert_gsc_ids(
  gsc,
  orgdb = "org.Hs.eg.db",
  from_type = NULL,
  to_type = "ENTREZID"
)

Arguments

gsc	geneSetCollection with IDs of a type one wishes to change.
orgdb	Annotation object containing the various IDs.
from_type	Name of the ID which your gsc is using. This can probably be automagically detected...
to_type	Name of the ID you wish to use.

Details

One caveat: this will collapse redundant IDs via unique().

Value

Fresh gene set collection replete with new names.

See Also

[AnnotationDbi] [guess_orgdb_keytypes()] [convert_ids()] [GSEABase]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.