cBioDataPack function allows the user to
download and process cancer study datasets found in MSKCC's cBioPortal.
Output datasets use the MultiAssayExperiment data
representation to faciliate analysis and data management operations.
cBioDataPack( cancer_study_id, use_cache = TRUE, names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene"), ask = TRUE )
character(1) The study identifier from cBioPortal as in https://cbioportal.org/webAPI
logical(1) (default TRUE) create the default cache location and use it to track downloaded data. If data found in the cache, data will not be re-downloaded. A path can also be provided to data cache location.
A character vector of possible column names for the column that is used to label ranges from a mutations or copy number file.
A logical vector of length one indicating whether to prompt the
the user before downloading and loading study
A MultiAssayExperiment object
The list of datasets can be found in the
data("studiesTable"). Some datasets may not be available
for download and are not guaranteed to be represented as MultiAssayExperiment
data objects. After taking a random sample of 100
set.seed(1234)), we were able to succesfully represent about
76 percent of the study identifiers as MultiAssayExperiment objects. Please
refer to the #' website for the
full list of available datasets. Users who would like to prioritize
particular datasets should open GitHub issues at the URL in the
file. For a more fine-grained approach to downloading data from the
cBioPortal API, refer to the
cBioDataPack function accesses data from the
By default, it points to an Amazon S3 bucket location. Previously, it
pointed to 'http://download.cbioportal.org'. This recent change
(> 2.1.17) should provide faster and more reliable downloads for all users.
See the URL using
cBioPortalData:::.url_location. This can be changed
if there are mirrors that host this data by setting the
getOption("cBio_URL", "https://some.url.com/") before running the
Levi Waldron, Marcel R., Ino dB.
#>  "paac_jhu_2014" "mel_tsam_liang_2017" "all_stjude_2015" #>  "all_stjude_2016" "aml_ohsu_2018" "laml_tcga"# ask=FALSE for non-interactive use mae <- cBioDataPack("acc_tcga", ask = FALSE)#>#>#>#>#>#>#>#>#>#>#>#>#>#> Warning: Multiple prefixes found, using keyword 'region' or taking first one#> Warning: Multiple prefixes found, using keyword 'region' or taking first one