getRegion-CellBaseR-method: getRegion

In melsiddieg/cellbaseR: Querying annotation data from the high performance Cellbase web

getRegion

Description

A method to query features within a genomic region from Cellbase web services.

Usage

## S4 method for signature 'CellBaseR'
getRegion(object, ids, resource, param = NULL)

Arguments

object	an object of class CellBaseR
ids	a character vector of the regions to be queried, for example, "1:1000000-1200000' should always be in the form 'chr:start-end'
resource	a character vector to specify the resource to be queried
param	a object of class CellBaseParam specifying additional param for the query

Details

This method retrieves various genomic features from a given region including genes, snps, clincally relevant variants, proteins, etc.

Value

a dataframe with the results of the query

See Also

https://github.com/opencb/cellbase/wiki and the RESTful API documentation http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/

Examples

   cb <- CellBaseR()
   res <- getRegion(object=cb, ids="17:1000000-1200000", resource="gene")

melsiddieg/cellbaseR documentation built on Jan. 16, 2024, 4:12 a.m.