remap_identifiers: Converts the feature identifiers in a GeneSetDb to a set of...

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

Description

The various GeneSetDb data providers limit the identifier types that they provide. Use this function to map the given identifiers to whichever type you like.

Usage

remap_identifiers(
  x,
  xref,
  original_id = colnames(xref)[1L],
  target_id = colnames(xref)[2L],
  ...
)

Arguments

x	The GeneSetDb with identifiers to convert
xref	If a species ("mouse" or "human") we will load the internal ensembl <-> entrez data.frame, or you can provide your own.

Details

You need to provie a data.frame that has a column for the current identifiers and another column for the target identifiers.

When there are multiple target id's for the source id, they will all be returned. When there is no target id for the source id, the soure feature will be axed.

By default, the first column of the xref data.frame is assumed to be the source identifiers, and the second is the target_id you want to remap the identifiers to.

Value

a remapped GeneSetDb object

Examples

gdb.entrez <- exampleGeneSetDb()
gdb.ens <- remap_identifiers(gdb.entrez, "human",
                             original_id = "entrezgene_id",
                             target_id = "ensembl_gene_id")

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.