map_orgdb_ids: Map AnnotationDbi keys from one column to another.

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

Map AnnotationDbi keys from one column to another.

Description

Given a couple of keytypes, this provides a quick mapping across them. I might have an alternate version of this hiding in the gsva code, which requires ENTREZIDs. In the mean time, this creates a dataframe of the mapped columns for a given set of gene ids using the in a sqlite instance.

Usage

map_orgdb_ids(orgdb, gene_ids = NULL, mapto = "ensembl", keytype = "geneid")

Arguments

orgdb	OrganismDb instance.
gene_ids	Gene identifiers for retrieving annotations.
mapto	Key to map the IDs against.
keytype	Choose a keytype, this will yell if it doesn't like your choice.

Value

a table of gene information

Author(s)

Keith Hughitt with changes by atb.

See Also

[AnnotationDbi]

Examples

 dm_unigene_to_ensembl <- map_orgdb_ids("org.Dm.eg.db", mapto = "ensembl", keytype = "unigene")
 head(dm_unigene_to_ensembl)

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