NEWS.md

In waldronlab/cBioPortalData: Exposes and Makes Available Data from the cBioPortal Web Resources

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

waldronlab/cBioPortalData documentation built on Jan. 15, 2025, 12:42 p.m.