makeTxDbFromMyGene: makeTxDbFromMyGene

Description Usage Arguments Details Value See Also Examples

View source: R/mygene.R

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

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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://mygene.info/doc/query_service.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

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

Bioconductor-mirror/mygene documentation built on June 1, 2017, 12:49 p.m.