- Defunct
removeDataCacheforcBioPortalDataas caching mechanism is no longer used. RuncBioCache()to get the cache location for deletion. Note thatcBioDataPackwill continue to cache data files at that location.
- Add
copyNumberDatahelper function tocBioPortalData - Add
studyIdargument to thefetchDatafunction - Use
molecularProfilesto determine mutation or copy number molecular profile type; previously this was deduced from the data name - Add example for filtering discrete copy number data
- Caching calls removed from
cBioPortalData. API requests will always be performed.cBioDataPackwill continue to cache data files. - Filter out
NULLparameters in internal.invoke_fun()API calls - Fix edge case in clinical data parsing when only a single file is present
- Update long unit tests expectations to reflect current study coverage (80%)
- Various documentation and example improvements
- Improvements to links in documentation and citation section in the vignette
- Remove error when
studyIdbuild success is unknown (@vlaufer, #69) - Parse tokens with different formats, e.g. genie token (@ZWael, #70)
- Clean up duplicate rows created in the
sampleMapgenerated from the data - Fixed warning trigger when empty
molecularProfileIddatasets are found
- Update
successratethresholds and fix long tests
- Add
cgdsrtocBioPortalDatamigration vignette (@kmezhoud, #54) - Unmapped experiments are now added to the metadata in
cBioDataPack - Set default
api. = api/v2/api-docsincBioPortalto access the API protocol's new location - The
fetchDatadeveloper function added to handle bothmolecularDataandmutationDatarequests as deduced from themolecularProfileIdsvector
- Check for valid
studyIds withgetStudiesincBioDataPack askargument correctly passed down to caching mechanism incBioDataPackcheck_buildoption available incBioDataPackparticularly for new studies that have not been checked against.
- Auth
tokenstring or file can now be included in thecBioPortalfunction. - The
check_buildargument can be set toFALSEfor alternative APIs, e.g., KidsFirst, when usingcBioPortalData queryGeneTabletranslates gene IDs ('hugoGeneSymbols' <> 'entrezGeneIds') via the API servicegetDataByGenessupersedesgetDataByGenePanelgetStudies()replacesdata('studiesTable')to discover study IDs
- Fixed issue where the
byargument was not passed togetDataByGenesin internal calls - Add names to metadata elements that originate from GISTIC datasets.
- A study's build status can be obtained from
getStudies(), which has replaceddata('studiesTable'). - Partial loading of data files supported. A warning is emitted when a
data file is not able to be loaded in
cBioDataPack. cBioPortalDatachecks thedata(studiesTable)to verify that study datasets are building, otherwise provide a message in interactive sessions.
- Vignettes include additional information (#38, @lwaldron)
getDataByGenePaneldeprecated forgetDataByGeneswhich handles input of both gene panels and genescBioPortalDatanow allows for gene inputs as either Entrez IDs or Hugo symbols (#24, @jucor) andsampleIdsinput- When
geneinputs are provided, thebyargument has to agree with the type of genes provided (either beentrezGeneIdorhugoGeneSymbol).
- Fixed an issue where the labels in the
metadatafromcBioDataPackwere missing ('LICENSE' and 'Fusion'; #37) loadStudyallowscleanup=TRUEfor removing files afteruntar-ing- Published article now available with
citation("cBioPortalData")
studiesTableincludes additional columnspack_buildandapi_buildto indicate to the user which datasets have been successfully built asMultiAssayExperimentobjects. Users will be notified when a dataset, reported as not building, is requested from thecBioDataPackfunction.- Add
sampleIdsargument togetDataByGenePanelas part of cache re-work - Allow more flexibility in the hostname when accessing the API with
cBioPortal(@inodb, #16) cBioDataPackdownloads from a more robust repository (AWS S3; @inodb, #22)removePackCacheandremoveDataCachenow remove data from the user's cache based on inputs to respective functions (cBioDataPackandcBioPortalData)
- Attempt to merge additional clinical data files from tarballs in
cBioDataPack. - Switch to using
read.deliminstead ofread_tsvinternally to avoid assigningNAto 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
cBioDataPackandcBioPortalDatain the documentation - Fix read-in when identifiers are numeric instead of character (@jucor, #27)
- Include pagination parameters in
geneTablefunction (@xinwei-sher, #29)
- Bioconductor release!
- Updated the
README.mdfile from R Markdown file. - Uses the latest version of
rapiclienton CRAN - Prepare package for Bioconductor submission
- Include protein metadata as a
RaggedExperimentfrom mutation molecular profiles (TCGA only)
- API authentication option removed and not needed
- Package supports nearly all study identifiers based on recent tests
- Only a handful of study identifiers are unsuccessful (create an issue to prioritize).
- Make better use of the API return values to craft the sample map for
MultiAssayExperimentcreation - Additional data included in the metadata slot of the
MultiAssayExperimentobject. Future revisions will include this data asrowData. - Change vignette titles for build
cBioDataPackallows users to download packaged data objects from download.cbioportal.org/- Data packs are cached using
BiocFileCacheto avoid re-downloading cBioPortalDatalets users query the cbioportal.org API and retrieve slices of data according to gene, molecular profile identifiers, etc.- Queries through
cBioPortalDatause a caching mechanism to avoid repeat downloads of data and improve load times - Both functions return a
MultiAssayExperimentas 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
AnVILpackage which makes use ofrapiclientto provide an automatic R interface to the API
- Data pack downloads use an alternative method for download when a download fails