Changes in version 2.10.0
New features
- Add cgdsr to cBioPortalData migration vignette (@kmezhoud, #54)
- Unmapped experiments are now added to the metadata in cBioDataPack
- Set default api. = api/v2/api-docs in cBioPortal to access the API
protocol's new location
- The fetchData developer function added to handle both molecularData
and mutationData requests as deduced from the molecularProfileIds
vector
Bug fixes and minor improvements
- Check for valid studyIds with getStudies in cBioDataPack
- ask argument correctly passed down to caching mechanism in
cBioDataPack
- check_build option available in cBioDataPack particularly for new
studies that have not been checked against.
Changes in version 2.8.0
New features
- Auth token string or file can now be included in the cBioPortal
function.
- The check_build argument can be set to FALSE for alternative APIs,
e.g., KidsFirst, when using cBioPortalData
- queryGeneTable translates gene IDs ('hugoGeneSymbols' <>
'entrezGeneIds') via the API service
- getDataByGenes supersedes getDataByGenePanel
- getStudies() replaces data('studiesTable') to discover study IDs
Bug fixes and minor improvements
- Fixed issue where the by argument was not passed to getDataByGenes
in internal calls
- Add names to metadata elements that originate from GISTIC datasets.
Changes in version 2.6.0
New features
- A study's build status can be obtained from getStudies(), which has
replaced data('studiesTable').
- Partial loading of data files supported. A warning is emitted when a
data file is not able to be loaded in cBioDataPack.
- cBioPortalData checks the data(studiesTable) to verify that study
datasets are building, otherwise provide a message in interactive
sessions.
Changes in version 2.4.0
New features
- Vignettes include additional information (#38, @lwaldron)
- getDataByGenePanel deprecated for getDataByGenes which handles input
of both gene panels and genes
- cBioPortalData now allows for gene inputs as either Entrez IDs or
Hugo symbols (#24, @jucor) and sampleIds input
- When gene inputs are provided, the by argument has to agree with the
type of genes provided (either be entrezGeneId or hugoGeneSymbol).
Bug fixes and minor improvements
- Fixed an issue where the labels in the metadata from cBioDataPack
were missing ('LICENSE' and 'Fusion'; #37)
- loadStudy allows cleanup=TRUE for removing files after untar-ing
- Published article now available with citation("cBioPortalData")
Changes in version 2.2.0
New features
- studiesTable includes additional columns pack_build and api_build to
indicate to the user which datasets have been successfully built as
MultiAssayExperiment objects. Users will be notified when a dataset,
reported as not building, is requested from the cBioDataPack
function.
- Add sampleIds argument to getDataByGenePanel as part of cache
re-work
- Allow more flexibility in the hostname when accessing the API with
cBioPortal (@inodb, #16)
- cBioDataPack downloads from a more robust repository (AWS S3;
@inodb, #22)
- removePackCache and removeDataCache now remove data from the user's
cache based on inputs to respective functions (cBioDataPack and
cBioPortalData)
Bug fixes and minor improvements
- Attempt to merge additional clinical data files from tarballs in
cBioDataPack.
- Switch to using read.delim instead of read_tsv internally to avoid
assigning NA to chromosome column
- Use 'PATIENT_ID' when available to determine if experiment data is
provided in the tarball files.
- Add tests using testthat
- Update and include percentages of studies successfully imported
using cBioDataPack and cBioPortalData in the documentation
- Fix read-in when identifiers are numeric instead of character
(@jucor, #27)
- Include pagination parameters in geneTable function (@xinwei-sher,
#29)
Changes in version 2.0.0
New features
- Bioconductor release!
- Updated the README.md file from R Markdown file.
- Uses the latest version of rapiclient on CRAN
- Prepare package for Bioconductor submission
- Include protein metadata as a RaggedExperiment from mutation
molecular profiles (TCGA only)
Bug fixes and minor improvements
- API authentication option removed and not needed
Changes in version 1.0.1
New features
- Package supports nearly all study identifiers based on recent tests
- Only a handful of study identifiers are unsuccessful (create an
issue to prioritize).
Bug fixes and minor improvements
- Make better use of the API return values to craft the sample map for
MultiAssayExperiment creation
- Additional data included in the metadata slot of the
MultiAssayExperiment object. Future revisions will include this data
as rowData.
- Change vignette titles for build
Changes in version 0.1.0
New features
- cBioDataPack allows users to download packaged data objects from
download.cbioportal.org/
- Data packs are cached using BiocFileCache to avoid re-downloading
- cBioPortalData lets users query the cbioportal.org API and retrieve
slices of data according to gene, molecular profile identifiers,
etc.
- Queries through cBioPortalData use a caching mechanism to avoid
repeat downloads of data and improve load times
- Both functions return a MultiAssayExperiment as the primary data
representation
- Only a number of study datasets are currently possible to load.
Issues can arise with mismatched or munged identifiers
- The cBioPortal API representation is handled by the AnVIL package
which makes use of rapiclient to provide an automatic R interface to
the API
Bug fixes and minor improvements
- Data pack downloads use an alternative method for download when a
download fails