cBioPortalData - GitHub Release 1.0.1

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

- R
Published by LiNk-NY over 6 years ago