getGenes: Return the list of gene objects for the given list of...

In biothings/mygene.R: Access MyGene.Info_ services

Description

This is a wrapper for POST query of "/gene" service.

Usage

getGenes(geneids, fields = c("symbol", "name", "taxid", "entrezgene"), ..., 
          return.as=c("DataFrame", "records", "text"), mygene)

Arguments

geneids	A vector, list, or comm-sep string entrez/ensembl gene ids
fields	A vector of fields to return. If fields=="all", all available fields are returned.
...	Includes species as well as several other fields. View available fields by calling ?metadata. Also, see http://docs.mygene.info/en/latest/doc/annotation_service.html for complete argument details and syntax.
return.as	"DataFrame" (default), "records" (list), "text" (JSON).
mygene	A MyGene object that describes how to connect to data resources. See MyGene-class. If missing, default object will be used that accesses the main MyGene.info portal. Default is recommended.

Value

returns a gene object (DataFrame, list, or JSON text) containing the queried annotations

References

Ref: http://docs.mygene.info/en/latest/doc/annotation_service.html

See Also

getGene query queryMany

Examples

## Return the list of gene object for the given list of gene ids.
getGenes(c(1017,1018))

## mix types of gene ids
getGenes(c(1017,1018,"ENSG00000148795"))

biothings/mygene.R documentation built on May 24, 2019, 3:04 a.m.