cBioPortalData: User Start Guide

knitr::opts_chunk$set(cache = TRUE)




This vignette lays out the two main user-facing functions for downloading and representing data from the cBioPortal API. cBioDataPack makes use of the legacy distribution data method in cBioPortal (via tarballs). cBioPortalData allows for a more flexibile approach to obtaining data based on several available parameters including available molecular profiles.

Two main interfaces

cBioDataPack: Obtain Study Data as Zipped Tarballs

This function will access the packaged data from \url{cBioPortal.org/datasets} and return an integrative MultiAssayExperiment representation.

## Use ask=FALSE for non-interactive use
cBioDataPack("laml_tcga", ask = FALSE)

cBioPortalData: Obtain data from the cBioPortal API

This function provides a more flexible and granular way to request a MultiAssayExperiment object from a study ID, molecular profile, gene panel, sample list.

cbio <- cBioPortal()
acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga",
    genePanelId = "IMPACT341",
    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")

Clearing the cache


In cases where a download is interrupted, the user may experience a corrupt cache. The user can clear the cache for a particular study by using the removeCache function. Note that this function only works for data downloaded through the cBioDataPack function.



For users who wish to clear the entire cBioPortalData cache, it is recommended that they use:




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cBioPortalData documentation built on April 17, 2021, 6:07 p.m.