keggLink: Find related entries by using database cross-references.

Description Usage Arguments Details Value Author(s) References Examples

Description

Find related entries by using database cross-references.

Usage

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keggLink(target, source)

Arguments

target

Either the name of a single KEGG database (list available via listDatabases(), a "T number" genome identifier, or a KEGG organism code (lists of both available via keggList("organism")).

source

The same as target, but may also be one or more KEGG identifiers.

Details

Many of the old KEGGSOAP functions whose names started with 'get', such as get.pathways.by.genes and get.pathways.by.reactions, are replaced by using keggLink (see examples).

Value

A named character vector.

Author(s)

Dan Tenenbaum

References

https://www.kegg.jp/kegg/docs/keggapi.html

Examples

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res <- keggLink("pathway", "hsa") ## KEGG pathways linked from each of
          ## the human genes equivalent to 'get.genes.by.pathway' in KEGGSOAP
length(res)
head(res)
res <- keggLink("hsa", "pathway") ## human genes linked from each of the
          ## KEGG pathways equivalent to 'get.pathways.by.genes' in KEGGSOAP
keggLink("pathway", c("hsa:10458", "ece:Z5100")) ## KEGG pathways
          ## linked from a human gene and an E. coli O157 gene
res <- keggLink("hsa:126") ## LinkDB search shows all KEGG
          ## resources related to hsa:126
head(res)

KEGGREST documentation built on May 6, 2019, 2:29 a.m.