MS_convertGene: Transform Entrez IDs or gene symbols into KEGG IDs

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This function allows transforming Entrez gene IDs or official gene symbols into KEGG IDs (orthology IDs or organism-specific gene IDs). The transformed KEGG IDs can be stored and used as source genes in the functions "MS_distances( )" or "MS_shortestpathsNetwork( )".

Usage

MS_convertGene(genes, organism_code, organism_name, output = "vector",
               orthology = TRUE)

Arguments

genes	character vector containing the Entrez IDs or official symbols of the genes of interest. All genes need to be in the same ID format (i.e. Entrez or symbols). It is preferable to use Entrez IDs rather than gene symbols, since some gene symbols are not unique.
organism_code	character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". See the function "MS_keggFinder( )".
organism_name	character vector containing the common name of the organism of interest (e.g. "rat", "mouse", "human", "zebrafish") or taxonomy id. For more details, check: http://docs.mygene.info/en/latest/doc/data.html#species. This argument is only required when gene symbols are used.
output	character constant indicating whether the function will return a vector containing mapped and transformed KEGG IDs (output = "vector"), or a matrix containing both mapped Entrez IDs or gene symbols and their corresponding KEGG IDs (output = "matrix").
orthology	logical scalar indicating whether the gene IDs will be transformed into orthology IDs or into organism-specific gene IDs.

Value

A character vector containing mapped and transformed KEGG IDs or a matrix containing both mapped Entrez IDs or gene symbols and their corresponding KEGG IDs.

References

Carlson, M. org.Hs.eg.db: Genome wide annotation for Human. R package version >= 3.2.3.

Mark, A., et al. (2014) mygene: Access MyGene.Info_ services. R package version >= 1.6.0.

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

Examples

# Transform gene symbol Hoga1 (293949) into rat-specific KEGG ID

MS_convertGene(genes = "Hoga1", organism_code = "rno", organism_name = "rat",
                  orthology = FALSE)

MS_convertGene(genes = "Hoga1", "rno", "rat", output = "matrix", orthology = FALSE)

# Transform entrez ID 293949 into orthology KEGG ID

MS_convertGene(genes = "293949", organism_code = "rno", output = "matrix")

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.