getClinical-CellBaseR-method: getClinical

getClinical,CellBaseR-methodR Documentation

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.