版本2.8.0的更改新功能 - cbioportal函数现在可以包含auth令牌字符串或文件。- check_build参数可以设置为false forse forsect for替代API，例如KidsFirst，当使用Cbioportaldata -QueryGenetable -QueryGenetable通过API服务 - getDatabygenes supersedeS suppersedeS supperseddatabygenepanel -getSties（）（）（）“ stitiestable”）发现研究IDS错误修复和较小的改进 - 修复了问题，该问题未传递到内部呼叫中的getDatabygenes - 将名称添加到源自GISTAT数据集的元数据元素中。版本2.6.0的更改新功能 - 可以从get -studies（）获得研究的构建状态，该状态已替换了数据（'Steciestable'）。- 支持支持的数据文件的部分加载。当数据文件无法在CBIodataPack中加载时，会发出警告。-CBIOPORTALDATA检查数据（setiestable）以验证研究数据集正在构建中，否则在交互式会话中提供了一条消息。版本2.4.0的更改新功能 - 小插图包括其他信息（＃38，@lwaldron） - getDatabygenepanel对GetDatabygenes进行了弃用，这些信息将基因面板和基因的输入处理 - Cbioportaldaldata -cbioportaldata -cbioportaldata现在允许将基因输入作为Entrez IDS或Hugo符号（＃＃24， @jucor）和sampleIds输入 - 当提供基因输入时，根据所提供的基因的类型（是胚胎或hugogenesymbol）。错误修复和较小的改进 - 修复了一个问题，其中cbiodatapack中元数据中的标签丢失（“许可证”和“融合”；＃37） - loadStudy允许清理= true true true用于删除untar -ing的文件 - 已发表的文章现在可用引用（“ CBIOPORTALDATA”）版本2.2.0新功能的更改 - setiestable包括其他列pack_build和api_build，以向用户指示数据集已成功构建为多亚sayexperiment对象。当从CBIODATAPACK函数请求未构建的数据集（报告为未构建）时，将通知用户。 - 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