新特性-研究的构建状态可以从getStudies()中获得，它取代了data('studiesTable')。—支持数据文件的部分加载。当数据文件无法加载到cBioDataPack中时，将发出警告。- cBioPortalData检查数据(studestable)，以验证研究数据集正在构建，否则在交互会话中提供消息。2.4.0版更改新特性- Vignettes包含额外信息(#38，@lwaldron) - getDataByGenePanel已弃用，用于处理基因面板和基因的输入- cBioPortalData现在允许基因输入为Entrez id或Hugo符号(#24，@jucor)和sampleIds输入-当提供基因输入时，by参数必须与所提供的基因类型一致(要么是entrezGeneId，要么是hugoGeneSymbol)。Bug修复和小的改进-修复了cBioDataPack元数据中标签缺失的问题('LICENSE'和'Fusion';#37) - loadStudy允许清除=TRUE删除文件后untar-已发布的文章现在可引用(“cBioPortalData”)2.2.0版的变化新功能- studestable包括额外的列pack_build和api_build，以指示用户哪些数据集已成功构建为MultiAssayExperiment对象。当cBioDataPack函数请求数据集(报告为未构建)时，用户将收到通知。-添加sampleIds参数到getDataByGenePanel作为缓存重新工作的一部分-当使用cBioPortal (@inodb， #16)访问API时，允许在主机名中具有更大的灵活性- cBioDataPack从更健壮的存储库(AWS S3;@inodb， #22) - removePackCache和removeDataCache现在根据输入到各自的函数(cBioDataPack和cBioPortalData)从用户的缓存中删除数据错误修复和微小的改进-尝试从cBioDataPack中的tarball合并额外的临床数据文件。 - 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