getVariant-CellBaseR-method: getVariant

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

getVariant

Description

A method to query variant annotation data from Cellbase web services from Cellbase web services.

Usage

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

Arguments

object	an object of class CellBaseR
ids	a character vector of the ids to be queried, must be in the following format 'chr:start:ref:alt', for example, '1:128546:A:T'
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 extensive genomic annotations for variants including consequence types, conservation data, population frequncies from 1k genomes and Exac projects, etc. as well as clinical data and various other annotations

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 <- getVariant(object=cb, ids="19:45411941:T:C", resource="annotation")

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