The 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"),
  cleanup = TRUE,
  ask = TRUE
)

Arguments

cancer_study_id

character(1) The study identifier from cBioPortal as in https://cbioportal.org/webAPI

use_cache

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.

names.field

A character vector of possible column names for the column that is used to label ranges from a mutations or copy number file.

cleanup

logical(1) whether to delete the untar-red contents from the exdir folder (default TRUE)

ask

A logical vector of length one indicating whether to prompt the the user before downloading and loading study MultiAssayExperiment. If TRUE, the user will be prompted to continue for studies that are not currently building as MultiAssayExperiment based on previous testing (in a non-interactive session, no data will be downloaded and built unless ask = FALSE).

Value

A MultiAssayExperiment object

Details

The full list of study identifiers (studyIds) can obtained from getStudies(). Currently, only ~ 72% of datasets can be represented as MultiAssayExperiment data objects from the data tarballs. Refer to getStudies(..., buildReport = TRUE) and its "pack_build" column to see which study identifiers are not building. Users who would like to prioritize particular datasets should open GitHub issues at the URL in the DESCRIPTION file. For a more fine-grained approach to downloading data from the cBioPortal API, refer to the cBioPortalData function.

cBio_URL

The cBioDataPack function accesses data from the cBio_URL option. 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 cBio_URL option with getOption("cBio_URL", "https://some.url.com/") before running the function.

See also

Author

Levi Waldron, Marcel R., Ino dB.

Examples


cbio <- cBioPortal()

head(getStudies(cbio)[["studyId"]])
#> [1] "nsclc_tcga_broad_2016" "hnsc_tcga"             "ov_tcga_pub"          
#> [4] "ucec_tcga_pub"         "blca_tcga_pub_2017"    "cesc_tcga"            

# ask=FALSE for non-interactive use
mae <- cBioDataPack("acc_tcga", ask = FALSE)
#> Study file in cache: acc_tcga
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_cna_hg19.seg
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_CNA.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_linear_CNA.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_methylation_hm450.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_mutations.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_mutsig.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_RNA_Seq_v2_expression_median.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_RNA_Seq_v2_mRNA_median_Zscores.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_rppa_Zscores.txt
#> Working on: /tmp/RtmpJ1XyZS/3202cd092fc_acc_tcga/acc_tcga/data_rppa.txt
#> Warning:  Multiple prefixes found, using keyword 'region' or taking first one
#> Warning:  Multiple prefixes found, using keyword 'region' or taking first one