alias2Gene: Convert gene aliases to standardized gene identifiers.

Description Usage Arguments Details Value Note See Also Examples

Description

Maps (potentially) obsolete gene names and nicknames to the current standard annotation.

Usage

1
2
alias2Gene(genes)
aliasGREP(genes)

Arguments

genes

A character vector of gene names and/or nicknames. In the case of aliasGREP, a vector of character patterns to search for.

Details

Uses the file "data/<speciesFilePrefix>.AliasTable.rda" from the DuffyTools installation folder as the reference source of alias details. Gene names that are not known or already standard nomenclature are returned unchanged. Standard names for Plasmodium species are from PlasmoDB.

Value

A vector the same length as genes, with the most current standard gene name for each gene.

Note

It is expected (but not enforced) that all geneID entries in the alias table exactly match the GeneIDs in the GeneMap for that species. The alias table used is determined by the current species.

See Also

gene2Alias

Examples

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  alias2Gene( c( "pfs25", "var2csa"))

robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.