R/cBioDataPack.R
cBioDataPack.RdThe 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 = interactive(),
check_build = 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.
character() Possible column names for the
column that will used to label ranges for data such as mutations or copy
number (default:
c("Hugo_Symbol", "Entrez_Gene_Id", "Gene", "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.
logical(1) whether to delete the untar-red contents from
the exdir folder (default TRUE)
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.
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'
A MultiAssayExperiment object
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.
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.
cbio <- cBioPortal()
head(getStudies(cbio)[["studyId"]])
#> [1] "acbc_mskcc_2015" "acyc_mskcc_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/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_cna.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_cna_hg19.seg
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_linear_cna.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_methylation_hm450.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_mutations.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_mutsig.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_acc_tcga/acc_tcga/data_rppa.txt
#> Working on: /tmp/RtmpN4OlPL/135067caa697_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