Title: | Exposes and Makes Available Data from the cBioPortal Web Resources |
---|---|
Description: | The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations. |
Authors: | Levi Waldron [aut], Marcel Ramos [aut, cre] , Karim Mezhoud [ctb] |
Maintainer: | Marcel Ramos <[email protected]> |
License: | AGPL-3 |
Version: | 2.19.2 |
Built: | 2024-11-18 21:27:56 UTC |
Source: | https://github.com/waldronlab/cBioPortalData |
Managing data downloads is important to save disk space and
avoid re-downloading data files. This can be done via the integrated
BiocFileCache
system.
cBioCache(..., ask = interactive()) setCache( directory = tools::R_user_dir("cBioPortalData", "cache"), verbose = TRUE, ask = interactive() ) removePackCache(cancer_study_id, dry.run = TRUE)
cBioCache(..., ask = interactive()) setCache( directory = tools::R_user_dir("cBioPortalData", "cache"), verbose = TRUE, ask = interactive() ) removePackCache(cancer_study_id, dry.run = TRUE)
... |
For |
ask |
logical (default TRUE when interactive session) Confirm the file location of the cache directory |
directory |
The file location where the cache is located. Once set future downloads will go to this folder. |
verbose |
Whether to print descriptive messages |
cancer_study_id |
character(1) The |
dry.run |
logical Whether or not to remove cache files (default TRUE). |
cBioCache: The path to the cache location
Get the directory location of the cache. It will prompt the user to create
a cache if not already created. A specific directory can be used via
setCache
.
Specify the directory location of the data cache. By default, it will go to the user directory as given by:
tools::R_user_dir("cBioPortalData", "cache")
Some files may become corrupt when downloading, this function allows
the user to delete the tarball associated with a cancer_study_id
in the
cache. This only works for the cBioDataPack
function. To remove the entire
cBioPortalData
cache, run unlink("~/.cache/cBioPortalData")
.
cBioCache() removePackCache("acc_tcga", dry.run = TRUE)
cBioCache() removePackCache("acc_tcga", dry.run = TRUE)
'cBioPortalData' no longer caches data from API responses; therefore, 'removeDataCache' is no longer needed. It will be removed as soon as the next release of Bioconductor.
removeDataCache( api, studyId = NA_character_, genePanelId = NA_character_, genes = NA_character_, molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, by = c("entrezGeneId", "hugoGeneSymbol"), dry.run = TRUE, ... )
removeDataCache( api, studyId = NA_character_, genePanelId = NA_character_, genes = NA_character_, molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, by = c("entrezGeneId", "hugoGeneSymbol"), dry.run = TRUE, ... )
api |
An API object of class 'cBioPortal' from the 'cBioPortal' function |
studyId |
character(1) Indicates the "studyId" as taken from 'getStudies' |
genePanelId |
character(1) Identifies the gene panel, as obtained from the 'genePanels' function |
genes |
character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses. |
molecularProfileIds |
character() A vector of molecular profile IDs |
sampleListId |
character(1) A sample list identifier as obtained from 'sampleLists()“ |
sampleIds |
character() Sample identifiers |
by |
character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId') |
dry.run |
logical Whether or not to remove cache files (default TRUE). |
... |
Additional arguments to lower level API functions |
removeDataCache: The path to the cache location when 'dry.run = FALSE' if the file exists. Otherwise, when 'dry.run = TRUE', the function return the output of the 'file.remove' operation.
Remove the computed cache location based on the function inputs to 'cBioPortalData()'. To remove the cache, simply replace the 'cBiocPortalData()' function name with 'removeDataCache()'; see the example. If the computed cache location is not found, it will return an empty vector.
cbio <- cBioPortal() cBioPortalData( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations") ) removeDataCache( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations"), dry.run = TRUE )
cbio <- cBioPortal() cBioPortalData( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations") ) removeDataCache( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations"), dry.run = TRUE )
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 = interactive(), check_build = TRUE )
cBioDataPack( cancer_study_id, use_cache = TRUE, names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene"), cleanup = TRUE, ask = interactive(), check_build = TRUE )
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 (default:
|
cleanup |
logical(1) whether to delete the |
ask |
logical(1) Whether to prompt the the user before downloading and
loading study |
check_build |
logical(1L) Whether to check the build status of the
|
The full list of study identifiers (studyId
s) 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.
A MultiAssayExperiment object
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.
Levi Waldron, Marcel R., Ino dB.
https://www.cbioportal.org/datasets, cBioPortalData, removePackCache
cbio <- cBioPortal() head(getStudies(cbio)[["studyId"]]) mae <- cBioDataPack("acc_tcga")
cbio <- cBioPortal() head(getStudies(cbio)[["studyId"]]) mae <- cBioDataPack("acc_tcga")
This section of the documentation lists the functions that allow users to access the cBioPortal API. The main representation of the API can be obtained from the 'cBioPortal' function. The supporting functions listed here give access to specific parts of the API and allow the user to explore the API with individual calls. Many of the functions here are listed for documentation purposes and are recommended for advanced usage only. Users should only need to use the 'cBioPortalData' main function to obtain data.
cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api. = "/api/v2/api-docs", token = character() ) getStudies(api, buildReport = FALSE) clinicalData(api, studyId = NA_character_) molecularProfiles( api, studyId = NA_character_, projection = c("SUMMARY", "ID", "DETAILED", "META") ) fetchData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) mutationData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) molecularData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) searchOps(api, keyword) samplesInSampleLists(api, sampleListIds = NA_character_) sampleLists(api, studyId = NA_character_) allSamples(api, studyId = NA_character_) getSampleInfo( api, studyId = NA_character_, sampleListIds = NULL, projection = c("SUMMARY", "ID", "DETAILED", "META") ) genePanels(api) getGenePanel(api, genePanelId = NA_character_) genePanelMolecular( api, molecularProfileId = NA_character_, sampleListId = NULL, sampleIds = NULL ) getGenePanelMolecular(api, molecularProfileIds = NA_character_, sampleIds) geneTable(api, pageSize = 1000, pageNumber = 0, ...) queryGeneTable( api, by = c("entrezGeneId", "hugoGeneSymbol"), genes = NA_character_, genePanelId = NA_character_ ) getDataByGenes( api, studyId = NA_character_, genes = NA_character_, genePanelId = NA_character_, by = c("entrezGeneId", "hugoGeneSymbol"), molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, ... )
cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api. = "/api/v2/api-docs", token = character() ) getStudies(api, buildReport = FALSE) clinicalData(api, studyId = NA_character_) molecularProfiles( api, studyId = NA_character_, projection = c("SUMMARY", "ID", "DETAILED", "META") ) fetchData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) mutationData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) molecularData( api, molecularProfileIds = NA_character_, entrezGeneIds = NULL, sampleIds = NULL ) searchOps(api, keyword) samplesInSampleLists(api, sampleListIds = NA_character_) sampleLists(api, studyId = NA_character_) allSamples(api, studyId = NA_character_) getSampleInfo( api, studyId = NA_character_, sampleListIds = NULL, projection = c("SUMMARY", "ID", "DETAILED", "META") ) genePanels(api) getGenePanel(api, genePanelId = NA_character_) genePanelMolecular( api, molecularProfileId = NA_character_, sampleListId = NULL, sampleIds = NULL ) getGenePanelMolecular(api, molecularProfileIds = NA_character_, sampleIds) geneTable(api, pageSize = 1000, pageNumber = 0, ...) queryGeneTable( api, by = c("entrezGeneId", "hugoGeneSymbol"), genes = NA_character_, genePanelId = NA_character_ ) getDataByGenes( api, studyId = NA_character_, genes = NA_character_, genePanelId = NA_character_, by = c("entrezGeneId", "hugoGeneSymbol"), molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, ... )
hostname |
character(1) The internet location of the service (default: 'www.cbioportal.org') |
protocol |
character(1) The internet protocol used to access the hostname (default: 'https') |
api. |
character(1) The directory location of the API protocol within the hostname (default: '/api/v2/api-docs') |
token |
character(1) The Authorization Bearer token e.g., "63eba81c-2591-4e15-9d1c-fb6e8e51e35d" or a path to text file. |
api |
An API object of class 'cBioPortal' from the 'cBioPortal' function |
buildReport |
logical(1) Indicates whether to append the build information to the 'getStudies()' table (default FALSE) |
studyId |
character(1) Indicates the "studyId" as taken from 'getStudies' |
projection |
character(default: "SUMMARY") Specify the projection type for data retrieval for details see API documentation |
molecularProfileIds |
character() A vector of molecular profile IDs |
entrezGeneIds |
numeric() A vector indicating entrez gene IDs |
sampleIds |
character() Sample identifiers |
keyword |
character(1) Keyword or pattern for searching through available operations |
sampleListIds |
character() A vector of 'sampleListId' as obtained from 'sampleLists' |
genePanelId |
character(1) Identifies the gene panel, as obtained from the 'genePanels' function |
molecularProfileId |
character(1) Indicates a molecular profile ID |
sampleListId |
character(1) A sample list identifier as obtained from 'sampleLists()“ |
pageSize |
numeric(1) The number of rows in the table to return |
pageNumber |
numeric(1) The pagination page number |
... |
Additional arguments to lower level API functions |
by |
character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId') |
genes |
character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses. |
cBioPortal: An API object of class 'cBioPortal'
cBioPortalData: A data object of class 'MultiAssayExperiment'
* getStudies - Obtain a table of studies and associated metadata and optionally include a 'buildReport' status (default FALSE) for each study. When enabled, the 'api_build' and 'pack_build' columns will be added to the table and will show if 'MultiAssayExperiment' objects can be generated for that particular study identifier ('studyId'). The 'api_build' column corresponds to datasets obtained with ‘cBioPortalData' and the ’pack_build' column corresponds to datsets loaded via 'cBioDataPack'.
* searchOps - Search through API operations with a keyword
* sampleLists - obtain all 'sampleListIds' for a particular 'studyId'
* allSamples - obtain all samples within a particular 'studyId'
* genePanels - Show all available gene panels
* geneTable - Get a table of all genes by 'entrezGeneId' and 'hugoGeneSymbol'
* queryGeneTable - Get a table for only the 'genes' or 'genePanelId' of interest. Gene inputs are identified with the 'by' argument
* clinicalData - Obtain clinical data for a particular study identifier ('studyId')
* molecularProfiles - Produce a molecular profiles dataset for a given study identifier ('studyId')
* fetchData - A convenience function to download both mutation and molecular data with 'molecularProfileId', 'entrezGeneIds', and 'sampleIds'
* mutationData - Produce a dataset of mutation data using 'molecularProfileId', 'entrezGeneIds', and 'sampleIds'
* molecularData - Produce a dataset of molecular profile data based on 'molecularProfileId', 'entrezGeneIds', and 'sampleIds'
* samplesInSampleLists - get all samples associated with a 'sampleListId'
* getSampleInfo - Obtain sample metadata for a particular 'studyId' or 'sampleListId'
* getGenePanels - Obtain the gene panel for a particular 'genePanelId'
* genePanelMolecular - get gene panel data for a particular 'molecularProfileId' and either a vector of 'sampleListId' or 'sampleId'
* getGenePanelMolecular - get gene panel data for multiple 'molecularProfileId's and a vector of 'sampleIds'
* getDataByGenes - Download data for a number of genes within 'molecularProfileId' indicators, optionally a 'sampleListId' can be provided.
cbio <- cBioPortal() getStudies(api = cbio) searchOps(api = cbio, keyword = "molecular") ## obtain clinical data acc_clin <- clinicalData(api = cbio, studyId = "acc_tcga") acc_clin molecularProfiles(api = cbio, studyId = "acc_tcga") genePanels(cbio) (gp <- getGenePanel(cbio, "AmpliSeq")) muts <- mutationData( api = cbio, molecularProfileIds = "acc_tcga_mutations", entrezGeneIds = 1:1000, sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01") ) exps <- molecularData( api = cbio, molecularProfileIds = c("acc_tcga_rna_seq_v2_mrna", "acc_tcga_rppa"), entrezGeneIds = 1:1000, sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01") ) sampleLists(api = cbio, studyId = "acc_tcga") samplesInSampleLists( api = cbio, sampleListIds = c("acc_tcga_rppa", "acc_tcga_cnaseq") ) genePanels(api = cbio) getGenePanel(api = cbio, genePanelId = "IMPACT341") queryGeneTable(api = cbio, by = "entrezGeneId", genes = 7157) clinicalData(cbio, "acc_tcga") getDataByGenes( cbio, studyId = "acc_tcga", genes = 1:3, by = c("entrezGeneId", "hugoGeneSymbol"), molecularProfileIds = "acc_tcga_rppa", sampleListId = "acc_tcga_rppa" )
cbio <- cBioPortal() getStudies(api = cbio) searchOps(api = cbio, keyword = "molecular") ## obtain clinical data acc_clin <- clinicalData(api = cbio, studyId = "acc_tcga") acc_clin molecularProfiles(api = cbio, studyId = "acc_tcga") genePanels(cbio) (gp <- getGenePanel(cbio, "AmpliSeq")) muts <- mutationData( api = cbio, molecularProfileIds = "acc_tcga_mutations", entrezGeneIds = 1:1000, sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01") ) exps <- molecularData( api = cbio, molecularProfileIds = c("acc_tcga_rna_seq_v2_mrna", "acc_tcga_rppa"), entrezGeneIds = 1:1000, sampleIds = c("TCGA-OR-A5J1-01", "TCGA-OR-A5J2-01") ) sampleLists(api = cbio, studyId = "acc_tcga") samplesInSampleLists( api = cbio, sampleListIds = c("acc_tcga_rppa", "acc_tcga_cnaseq") ) genePanels(api = cbio) getGenePanel(api = cbio, genePanelId = "IMPACT341") queryGeneTable(api = cbio, by = "entrezGeneId", genes = 7157) clinicalData(cbio, "acc_tcga") getDataByGenes( cbio, studyId = "acc_tcga", genes = 1:3, by = c("entrezGeneId", "hugoGeneSymbol"), molecularProfileIds = "acc_tcga_rppa", sampleListId = "acc_tcga_rppa" )
The cBioPortal
class is a representation of the cBioPortal
API protocol that directly inherits from the Service
class in the
AnVIL
package. For more information, see the
AnVIL package.
## S4 method for signature 'cBioPortal' operations(x, ..., .deprecated = FALSE)
## S4 method for signature 'cBioPortal' operations(x, ..., .deprecated = FALSE)
x |
A Service instance or API representation as given by the cBioPortal function. |
... |
additional arguments passed to methods or, for
|
.deprecated |
optional logical(1) include deprecated operations? |
This class takes the static API as provided at https://www.cbioportal.org/api/v2/api-docs and creates an R object with the help from underlying infrastructure (i.e., rapiclient and AnVIL) to give the user a unified representation of the API specification provided by the cBioPortal group. Users are not expected to interact with this class other than to use it as input to the functionality provided by the rest of the package.
A cBioPortal
class instance
operations(cBioPortal)
:
cBioPortal()
cBioPortal()
Obtain a MultiAssayExperiment
object for a particular gene panel,
studyId
, molecularProfileIds
, and sampleListIds
combination. Default
molecularProfileIds
and sampleListIds
are set to NULL for including all
data. This option is best for users who wish to obtain a section of the
study data that pertains to a specific molecular profile and gene panel
combination. For users looking to download the entire study data as provided
by the https://www.cbioportal.org/datasets, refer to cBioDataPack
.
cBioPortalData( api, studyId = NA_character_, genePanelId = NA_character_, genes = NA_character_, molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, by = c("entrezGeneId", "hugoGeneSymbol"), check_build = TRUE, ask = interactive() )
cBioPortalData( api, studyId = NA_character_, genePanelId = NA_character_, genes = NA_character_, molecularProfileIds = NULL, sampleListId = NULL, sampleIds = NULL, by = c("entrezGeneId", "hugoGeneSymbol"), check_build = TRUE, ask = interactive() )
api |
An API object of class 'cBioPortal' from the 'cBioPortal' function |
studyId |
character(1) Indicates the "studyId" as taken from 'getStudies' |
genePanelId |
character(1) Identifies the gene panel, as obtained from the 'genePanels' function |
genes |
character() Either Entrez gene identifiers or Hugo gene symbols. When included, the 'by' argument indicates the type of identifier provided and 'genePanelId' is ignored. Preference is given to Entrez IDs due to faster query responses. |
molecularProfileIds |
character() A vector of molecular profile IDs |
sampleListId |
character(1) A sample list identifier as obtained from 'sampleLists()“ |
sampleIds |
character() Sample identifiers |
by |
character(1) Either 'entrezGeneId' or 'hugoGeneSymbol' for row metadata (default: 'entrezGeneId') |
check_build |
logical(1L) Whether to check the build status of the
|
ask |
logical(1) Whether to prompt the the user before downloading and
loading study |
We are able to succesfully represent 98 percent of the study
identifiers as MultiAssayExperiment
objects as obtained via
cBioPortalData
with the IMPACT341
genePanelId
as the example
gene panel. Datasets that currently fail to import
can be seen in the getStudies(..., buildReport = TRUE)
dataset
under the "api_build"
column.
Note that changes to the cBioPortal API may affect this rate at any
time. If you encounter any issues, please open a GitHub issue at the
https://github.com/waldronlab/cBioPortalData/issues/ page with
a fully reproducible example.
A MultiAssayExperiment object
cbio <- cBioPortal() samps <- samplesInSampleLists(cbio, "acc_tcga_rppa")[[1]] getGenePanelMolecular( cbio, molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA"), samps ) acc_tcga <- cBioPortalData( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations") )
cbio <- cBioPortal() samps <- samplesInSampleLists(cbio, "acc_tcga_rppa")[[1]] getGenePanelMolecular( cbio, molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA"), samps ) acc_tcga <- cBioPortalData( cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "AmpliSeq", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations") )
Note that these functions should be used when a particular
study is not currently available as a MultiAssayExperiment
representation. Otherwise, use cBioDataPack
. Provide a cancer_study_id
from getStudies
and retrieve the study tarball from the cBio
Genomics Portal. These functions are used by cBioDataPack
under the hood
to download,untar, and load the tarball datasets with caching. As stated in
?cBioDataPack
, not all studies are currently working as
MultiAssayExperiment
objects. As of July 2020, about ~80% of
datasets can be successfully imported into the MultiAssayExperiment
data
class. Please open an issue if you would like the team to prioritize a
study. You may also check getStudies(buildReport = TRUE)$pack_build
for the current status.
downloadStudy( cancer_study_id, use_cache = TRUE, force = FALSE, url_location = getOption("cBio_URL", .url_location), ask = interactive() ) untarStudy(cancer_study_file, exdir = tempdir()) loadStudy( filepath, names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene", "Composite.Element.REF"), cleanup = TRUE )
downloadStudy( cancer_study_id, use_cache = TRUE, force = FALSE, url_location = getOption("cBio_URL", .url_location), ask = interactive() ) untarStudy(cancer_study_file, exdir = tempdir()) loadStudy( filepath, names.field = c("Hugo_Symbol", "Entrez_Gene_Id", "Gene", "Composite.Element.REF"), cleanup = TRUE )
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. |
force |
logical(1) (default FALSE) whether to force re-download data from remote location |
url_location |
character(1)
(default "https://cbioportal-datahub.s3.amazonaws.com") the URL location for
downloading packaged data. Can be set using the 'cBio_URL' option (see
|
ask |
logical(1) Whether to prompt the the user before downloading and
loading study |
cancer_study_file |
character(1) indicates the on-disk location of the downloaded tarball |
exdir |
character(1) indicates the folder location to put
the contents of the tarball (default |
filepath |
character(1) indicates the folder location where
the contents of the tarball are located (usually the same as |
names.field |
character() Possible column names for the
column that will used to label ranges for data such as mutations or copy
number (default:
|
cleanup |
logical(1) whether to delete the |
When attempting to load a dataset using loadStudy
, note that
the cleanup
argument is set to TRUE
by default. Change the argument
to FALSE
if you would like to keep the untarred data in the exdir
location. downloadStudy
and untarStudy
are not affected by this change.
The tarball of the downloaded data is cached via BiocFileCache
when
use_cache
is TRUE
.
downloadStudy - The file location of the data tarball
untarStudy - The directory location of the contents
loadStudy - A MultiAssayExperiment-class object
cBioDataPack, MultiAssayExperiment
(acc_file <- downloadStudy("acc_tcga")) (file_dir <- untarStudy(acc_file, tempdir())) loadStudy(file_dir)
(acc_file <- downloadStudy("acc_tcga")) (file_dir <- untarStudy(acc_file, tempdir())) loadStudy(file_dir)