pathview (version 1.12.0)

eg2id: Mapping between different gene ID and annotation types

Description

These auxillary gene ID mappers connect different gene ID or annotation types, especially they are used to map 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, ...)
geneannot.map(in.ids, in.type, out.type, org="Hs", pkg.name=NULL,
unique.map=TRUE, na.rm=TRUE, keep.order=TRUE)

Arguments

eg

character, input Entrez Gene IDs.

ids

character, input gene/transcript/protein IDs to be converted to Entrez Gene IDs.

in.ids

character, input gene/transcript/protein IDs to be converted or mapped to other Gene IDs or annotation types.

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".

in.type

character, the input gene/transcript/protein ID type to be mapped or converted to other ID/annotation types.

out.type

character, the output gene/transcript/protein ID type to be mapped or converted to other ID/annotation types.

org

character, the two-letter abbreviation of organism name, or KEGG species code, or the common species name, used to determine the gene annotation package. For all potential values check: data(bods); bods. Default org="Hs", and can also be "hsa" or "human" (case insensitive). 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.

unique.map

logical, whether to combine multiple entries mapped to the same input ID as a single entry (separted by "; "). Default unique.map=TRUE.

na.rm

logical, whether to remove the lines where input ID is not mapped (NA for mapped entries). Default na.rm=TRUE.

keep.order

logical, whether to keep the original input order even with all unmapped input IDs. Default keep.order=TRUE.

...

other arguments to be passed to geneannot.map function.

Value

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

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. Both id2eg and eg2id are wrapper functions of geneannot.map function. The latter can be used to map between a range of major gene/transcript/protein IDs or annotation types, not just Entrez Gene ID. 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.

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)

#not run: map between other ID types for other species
#ath.tair=sim.mol.data(id.type="tair", species="ath", nmol=1000)
#data(gene.idtype.bods)
#gid.map <-geneannot.map(in.ids=names(ath.tair)[rep(1:100,each=2)],
#in.type="tair", out.type=gene.idtype.bods$ath[-1], org="At")
#gid.map1 <-geneannot.map(in.ids=names(ath.tair)[rep(1:100,each=2)],
#in.type="tair", out.type=gene.idtype.bods$ath[-1], org="At",
#unique.map=F, keep.order=F)
#str(gid.map)
#str(gid.map1)