NEWS.md

In cBioPortalData: Exposes and makes available data from the cBioPortal web resources

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

cBioPortalData documentation built on April 17, 2021, 6:07 p.m.