cbio.query: cbio.query

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

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.

TRONCO documentation built on Nov. 8, 2020, 5:51 p.m.