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 2.25.1 Index]