makeTxDbFromMyGene: makeTxDbFromMyGene

In mygene: Access MyGene.Info_ services

Description

makeTxDbFromMyGene allows the user to make a TxDb object in the Genomic Features package from a mygene "exons" query using a default MyGene object.

Usage

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

Arguments

gene.list	A list, vector, or comma-separated string of query terms.
scopes	Type of types of identifiers, either a list, vector, or a comma-separated fields to specify type of input qterms, e.g. c("reporter", "ensembl.gene", "symbol") refer to "http://docs.mygene.info/en/latest/doc/data.html#available-fields" for full list of fields.
species	Names or taxonomy ids
returnall	Logical, if TRUE, return list of genes without exons annotations. False by Default.

Details

makeTxDbFromMyGene invokes either the query or queryMany method and passes the response to construct a TxDb object. See ?TxDb for utilizing transcript annotations.

Value

returns TxDb object

See Also

makeTxDb

Examples

xli <- c('DDX26B','CCDC83','MAST3', 'RPL11')
txdb <- makeTxDbFromMyGene(xli, scopes="symbol", species="human")

mygene documentation built on Nov. 8, 2020, 5:38 p.m.