Obtain pre-packaged data from cBioPortal and represent as a MultiAssayExperiment object

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.

Usage

cBioDataPack(
  cancer_study_id,
  use_cache = TRUE,
  names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene"),
  cleanup = TRUE,
  ask = interactive(),
  check_build = TRUE
)

Arguments

cancer_study_id

character(1) The study identifier from cBioPortal as seen in the dataset links at https://www.cbioportal.org/datasets.

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

character() Possible column names for the column that will used to label ranges for data such as mutations or copy number (defaults: "Hugo_Symbol", "Entrez_Gene_Id", "Gene", and "Composite.Element.REF"). Values are cycled through and eliminated when no data present, or duplicates are found. Values in the corresponding column must be unique in each row.

cleanup

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

ask

logical(1) Whether to prompt the the user before downloading and loading study MultiAssayExperiment that is not currently building based on previous testing. Set to interactive() by default. In a non-interactive session, data download will be attempted; equivalent to ask = FALSE. The argument will also be used when a cache directory needs to be created when using downloadStudy.

check_build

logical(1L) Whether to check the build status of the studyId using an internal dataset. This argument should be set to FALSE if using alternative hostnames, e.g., 'pedcbioportal.kidsfirstdrc.org'

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

https://www.cbioportal.org/datasets, cBioPortalData, removePackCache

Author

Levi Waldron, Marcel R., Ino dB.

Examples

cbio <- cBioPortal()

head(getStudies(cbio)[["studyId"]])
#> [1] "all_stjude_2015" "all_stjude_2013" "acyc_fmi_2014"   "acyc_jhu_2016"  
#> [5] "acyc_mda_2015"   "acyc_mgh_2016"  

mae <- cBioDataPack("acc_tcga")
#> Study file in cache: acc_tcga
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_cna.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_cna_hg19.seg
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_linear_cna.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_methylation_hm450.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_mutations.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_mutsig.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_rppa.txt
#> Working on: /tmp/RtmpdbKWbS/a1d7e2b6e07_acc_tcga/acc_tcga/data_rppa_zscores.txt
#> Warning:  Multiple prefixes found, using keyword 'region' or taking first one
#> Warning:  Multiple prefixes found, using keyword 'region' or taking first one