NEWS

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cBioPortalData 2.22.0

New features

• Defunct removeDataCache for cBioPortalData as caching mechanism is no longer used. Run cBioCache() to get the cache location for deletion. Note that cBioDataPack will continue to cache data files at that location.

cBioPortalData 2.20.0

New features

• Add copyNumberData helper function to cBioPortalData
• Add studyId argument to the fetchData function
• Use molecularProfiles to determine mutation or copy number molecular profile type; previously this was deduced from the data name
• Add example for filtering discrete copy number data

Bug fixes and minor improvements

• Caching calls removed from cBioPortalData. API requests will always be performed. cBioDataPack will continue to cache data files.
• Filter out NULL parameters in internal .invoke_fun() API calls
• Fix edge case in clinical data parsing when only a single file is present
• Update long unit tests expectations to reflect current study coverage (80%)
• Various documentation and example improvements

cBioPortalData 2.16.0

Bug fixes and minor improvements

• Improvements to links in documentation and citation section in the vignette

cBioPortalData 2.14.0

Bug fixes and minor improvements

• Remove error when studyId build success is unknown (@vlaufer, #69)
• Parse tokens with different formats, e.g. genie token (@ZWael, #70)
• Clean up duplicate rows created in the sampleMap generated from the data
• Fixed warning trigger when empty molecularProfileId datasets are found

cBioPortalData 2.12.0

Bug fixes and minor improvements

• Update successrate thresholds and fix long tests

cBioPortalData 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.

cBioPortalData 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.

cBioPortalData 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.

cBioPortalData 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")

cBioPortalData 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)

cBioPortalData 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

cBioPortalData 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

cBioPortalData 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