In waldronlab/cBioPortalData: Exposes and Makes Available Data from the cBioPortal Web Resources

knitr::opts_chunk$set(cache = TRUE)

Loading

library(cBioPortalData)
library(AnVIL)
library(jsonlite)

Overview

This document serves as a reporting tool for errors that occur when running our utility functions on the cBioPortal datasets.

Data from the cBioPortal API (cBioPortalData())

Typically, the number of errors encountered via the API are low. There are only a handful of packages that error when we apply the utility functions to provide a MultiAssayExperiment data representation.

First, we load the error Rda dataset.

api_errs <- system.file(
    "extdata", "api", "err_api_info.json",
    package = "cBioPortalData", mustWork = TRUE
)
err_api_info <- fromJSON(api_errs)

We can now inspect the contents of the data:

class(err_api_info)
length(err_api_info)
lengths(err_api_info)

There were about r length(err_api_info) unique errors during the last build run.

names(err_api_info)

The most common error was Inconsistent build numbers found. This is due to annotations from different build numbers that were not able to be resolved.

To see what datasets (cancer_study_id s) have that error we can use:

err_api_info[['Inconsistent build numbers found']]

We can also have a look at the entirety of the dataset.

err_api_info

Packaged data from cBioDataPack()

Now let's look at the errors in the packaged datasets that are used for cBioDataPack:

pack_errs <- system.file(
    "extdata", "pack", "err_pack_info.json",
    package = "cBioPortalData", mustWork = TRUE
)
err_pack_info <- fromJSON(pack_errs)

We can do the same for this data:

length(err_pack_info)
lengths(err_pack_info)

We can get a list of all the errors present:

names(err_pack_info)

And finally the full list of errors:

err_pack_info

sessionInfo

sessionInfo()

waldronlab/cBioPortalData documentation built on Jan. 15, 2025, 12:42 p.m.