eg2id: Mapping between Entrez Gene and other IDs

In pathview: a tool set for pathway based data integration and visualization

Description

These auxillary gene ID mappers connect Entrez Gene ID to external gene, transcript or protein IDs or vise versa.

Usage

eg2id(eg, category = gene.idtype.list[1:2], org = "Hs", pkg.name = NULL)
id2eg(ids, category = gene.idtype.list[1], org = "Hs", pkg.name = NULL)

Arguments

eg	character, input Entrez Gene IDs.
ids	character, input gene/transcript/protein IDs to be converted to Entrez Gene IDs.
category	character, for eg2id the output ID types to map from Entrez Gene, d to be c("SYMBOL", "GENENAME"); for id2eg, the input ID type to be mapped to Entrez Gene, default to be "SYMBOL".
org	character, the two-letter abbreviation of organism name, used to determine the gene annotation package. Default org="Hs". Only effective when pkg.name is not NULL.
pkg.name	character, name of the gene annotation package. This package should be one of the standard annotation packages from Bioconductor, such as "org.Hs.eg.db". Check data(bods); bods for a full list of standard annotation packages. You may also use your custom annotation package built with AnnotationDbi, the Bioconductor Annotation Database Interface. Default pkg.name=NULL, hence argument org should be specified.

Details

KEGG uses Entrez Gene ID as its standard gene ID. Therefore, all gene data need to be mapped to Entrez Genes when working with KEGG pathways. Function id2eg does this mapping. On the other hand, we frequently want to check or show gene symbols or full names instead of the less informative Entrez Gene ID when working with KEGG gene nodes, Function eg2id does this reverse mapping. These functions are written as part of the Pathview mapper module, they are equally useful for other gene ID or data mapping tasks. The use of these functions depends on gene annotation packages like "org.Hs.eg.db", which are Bioconductor standard. IFf no such packages not available for your interesting organisms, you may build one with Bioconductor AnnotationDbi package.

Value

a 2- or multi-column character matrix recording the mapping between input IDs to the target ID type(s).

Author(s)

Weijun Luo <[e-mail]>

References

Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285

See Also

cpd2kegg etc the auxillary compound ID mappers, mol.sum the auxillary molecular data mapper, node.map the node data mapper function.

Examples

data(gene.idtype.list)
#generate simulated gene data named with non-KEGG/Entrez gene IDs
gene.ensprot <- sim.mol.data(mol.type = "gene", id.type = gene.idtype.list[4], 
    nmol = 50000)
#construct map between non-KEGG ID and KEGG ID (Entrez gene)
id.map.ensprot <- id2eg(ids = names(gene.ensprot), 
    category = gene.idtype.list[4], org = "Hs")
#Map molecular data onto Entrez Gene IDs
gene.entrez <- mol.sum(mol.data = gene.ensprot, id.map = id.map.ensprot)
#check the results
head(gene.ensprot)
head(id.map.ensprot)
head(gene.entrez)

#map Entrez Gene to Gene Symbol and Name
eg.symbname=eg2id(eg=id.map.ensprot[,2])
#entries with more than 1 Entrez Genes are not mapped
head(eg.symbname)

pathview documentation built on May 2, 2019, 4:56 p.m.