% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/cBioDataPack.R
\name{cBioDataPack}
\alias{cBioDataPack}
\title{Obtain pre-packaged data from cBioPortal and represent as
a MultiAssayExperiment object}
\usage{
cBioDataPack(
  cancer_study_id,
  use_cache = TRUE,
  names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene"),
  cleanup = TRUE,
  ask = TRUE
)
}
\arguments{
\item{cancer_study_id}{character(1) The study identifier from cBioPortal as
in \url{https://cbioportal.org/webAPI}}

\item{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.}

\item{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.}

\item{cleanup}{logical(1) whether to delete the \code{untar}-red contents from
the \code{exdir} folder (default TRUE)}

\item{ask}{A logical vector of length one indicating whether to prompt the
the user before downloading and loading study \code{MultiAssayExperiment}. If
TRUE, the user will be prompted to continue for studies that are not
currently building as \code{MultiAssayExperiment} based on previous testing
(in a non-interactive session, no data will be downloaded and built unless
\code{ask = FALSE}).}
}
\value{
A \linkS4class{MultiAssayExperiment} object
}
\description{
The \code{cBioDataPack} function allows the user to
download and process cancer study datasets found in MSKCC's cBioPortal.
Output datasets use the \linkS4class{MultiAssayExperiment} data
representation to faciliate analysis and data management operations.
}
\details{
The list of datasets can be found in the \code{studiesTable} dataset
by doing \code{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
(using \code{set.seed(1234)}), we were able to succesfully represent about
76 percent of the study identifiers as MultiAssayExperiment objects. Please
refer to the #' \href{http://cbioportal.org/data_sets.jsp}{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 \code{DESCRIPTION}
file. For a more fine-grained approach to downloading data from the
cBioPortal API, refer to the \code{cBioPortalData} function.
}
\section{cBio_URL}{

The \code{cBioDataPack} function accesses data from the \code{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 \code{cBioPortalData:::.url_location}. This can be changed
if there are mirrors that host this data by setting the \code{cBio_URL} option
with \code{getOption("cBio_URL", "https://some.url.com/")} before running the
function.
}

\examples{

data(studiesTable)

head(studiesTable[["cancer_study_id"]])

# ask=FALSE for non-interactive use
mae <- cBioDataPack("acc_tcga", ask = FALSE)

}
\seealso{
\url{https://www.cbioportal.org/datasets}, \link{cBioPortalData}
}
\author{
Levi Waldron, Marcel R., Ino dB.
}