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NEWS.md

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Changes in version 2.20.0

New features

  • Caching calls removed from cBioPortalData. API requests will always be performed. cBioDataPack will continue to cache data files.

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