EnsemblStuff: Map gene names

In tallulandrews/CycleMix: Cell-Cycle using Mixture Models

Map gene names

Description

Mapping human and mouse genes to HGNC or MGI gene symbols or across species.

Usage

  downloadEnsemblData(host="www.ensembl.org")
  mapGeneNames(maps, genes, in.org=c("Hsap","Mmus"), in.name=c("symbol","ensg"), out.org=c("Hsap","Mmus"), out.name=c("symbol","ensg"))

Arguments

host	URL to download ensembl data from (e.g. archive vs current).
maps	output from downloadEnsemblData.
genes	vector of gene IDs.
in.org	organism of input genes.
in.name	input gene ID type.
out.org	desired organism for output genes.
out.name	desired ID type for output.

Details

downloadEnsemblData: Downloads gene ids and orthologs for all protein-coding genes from ensembl biomart. mapGeneNames: Converts genes from one type to another or to orthologs in the other species.

Value

The input SingleCellExperiment object with the regressed expression saved to the 'norm_exprs' slot.

Examples

	maps <- downloadEnsemblData();

	# Convert Whitfield CC table for use in mouse
	MGeneSets$Whitfield <- HGeneSets$Whitfield
	MGeneSets$Whitfield$Gene <- mapGeneNames(maps, as.character(MGeneSets$Whitfield$Gene), in.org="Hsap", in.name="symbol", out.org="Mmus", out.name="symbol")
	MGeneSets$Whitfield <- MGeneSets$Whitfield[MGeneSets$Whitfield$Gene != "",] #remove genes without orthologs.

tallulandrews/CycleMix documentation built on Sept. 28, 2022, 6:55 p.m.