MyGene-class: Class '"MyGene"'

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

Description

R Client to access MyGene.Info annotation services

Objects from the Class

Objects can be created by calls of the form MyGene(base.url="http://mygene.info/v2", delay=1, step=1000, version=version, verbose=TRUE, debug=FALSE).

Slots

base.url:

"http://mygene.info/v2". Object of class "character"

delay:

Sleep time between batch retrieval. Object of class "numeric"

step:

Batch limit. Object of class "numeric"

version:

httr package version. Object of class "character"

verbose:

Object of class "logical"

debug:

Object of class "logical"

Methods

getGene(geneid, fields = c("symbol", "name", "taxid", "entrezgene"), ..., return.as=c("records", "text")):

Return the gene object for the given geneid

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

Return the list of gene object for the given list of geneids.

query(q, fields=c("name", "symbol", "taxid", "entrezgene"), ..., return.as=c("DataFrame", "records", "text")):

Return the query result.

queryMany(qterms, scopes=NULL, fields=c("name", "symbol", "taxid", "entrezgene"), ..., return.as=c("DataFrame", "records", "text"), returnall=FALSE):

Return the batch query result.

metadata(x, ...):

Get metadata for MyGene.info services.

makeTxDbFromMyGene(gene.list, scopes, species, returnall=FALSE):

Make a TxDb object from transcript annotations

Author(s)

Adam Mark, Chunlei Wu, Ryan Thompson

References

Wu C, MacLeod I, Su AI (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucl. Acids Res. 41(D1): D561-D565.

Examples

showClass("MyGene")

SuLab/mygene.R documentation built on May 9, 2019, 3:22 p.m.