getClinical-CellBaseR-method: getClinical

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

getClinical

Description

A method to query Clinical data from Cellbase web services.

Usage

## S4 method for signature 'CellBaseR'
getClinical(object, param = NULL)

Arguments

object	an object of class CellBaseR
param	a object of class CellBaseParam specifying the parameters limiting the CellBaseR

Details

This method retrieves clinicaly relevant variants annotations from multiple resources including clinvar, cosmic and gwas catalog. Furthermore, the user can filter these data in many ways including trait, features, rs, 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()
   cbParam <- CellBaseParam(feature=c("TP73","TET1"), limit=100)
   res <- getClinical(object=cb,param=cbParam)

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