Changes in version 2.16.0 Bug fixes and minor improvements - Improvements to links in documentation and citation section in the vignette Changes in version 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 Changes in version 2.12.0 Bug fixes and minor improvements - Update successrate thresholds and fix long tests 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