cbio.query {TRONCO} | R Documentation

## cbio.query

### Description

Wrapper for the CGDS package to query the Cbio portal. This can work either automatically, if one sets `cbio.study`, `cbio.dataset` or `cbio.profile`, or interactively otherwise. A list of genes to query with less than 900 entries should be provided. This function returns a list with two dataframe: the gentic profile required and clinical data for the Cbio study. Output is also saved to disk as Rdata file. See also http://www.cbioportal.org.

### Usage

    cbio.query(
      cbio.study = NA,
      cbio.dataset = NA,
      cbio.profile = NA,
      genes,
      file = NA
    )

### Arguments

`cbio.study` | Cbio study ID
`cbio.dataset` | Cbio dataset ID
`cbio.profile` | Cbio genetic profile ID
`genes` | A list of < 900 genes to query
`file` | String containing filename for RData output. If NA no output will be provided

### Value

A list with two dataframe: the gentic profile required and clinical data for the Cbio study.

[Package TRONCO version 2.20.1 Index]