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Changes in version 1.24.0
Significant User-visible changes
The legacy argument in ID translation functions (UUIDtoBarcode, UUIDtoUUID, barcodeToUUID, and filenameToBarcode) has been defunct and removed.
Bug fixes and minor improvements
UUIDtoBarcode ensures that results are ordered based on the input UUIDs.
Include informative error message regarding translation of UUIDs from legacy files.
Changes in version 1.22.0
Bug fixes and minor improvements
UUIDtoBarcode returns barcodes consistent with Genomic Data Commons API update
Changes in version 1.20.0
New features
makeSummarizedExperimentFromGISTIC and splitAssays are now defunct.
Minor changes and bug fixes
makeGRangesListFromExonFiles example removed from the vignette, the GDC legacy endpoint has been deprecated. For more information see the GDC API release notes version v3.28.0.
Changes in version 1.18.0
Minor changes and bug fixes
Use https instead of http in getFileName helper.
Warn when column names in assays are not mappable and subsequently dropped in generateMap.
Updated qreduceTCGA documentation for clarity.
Changes in version 1.16.0
New features
The UUIDhistory function allows users to map old UUIDs to new UUIDs according to the latest data release for UUIDs that were affected and no longer query-able.
The slides argument has been added to the filenameToBarcode function for translating slide file names into barcodes. Currently, the API returns all barcodes of the associated case ID.
Add sections in the vignette regarding GDC Data Updates and UUID history lookup
Minor changes and bug fixes
Update examples in package to new GDC Data Release, see vignette.
Use AnnotationHub to download chain file in main vignette.
Slide file names now resolve to a single TCGA barcode in filenameToBarcode (Thanks @hermidalc )
Improved error messages and documentation for makeGRangesListFromExonFiles
Changes in version 1.14.0
Minor changes and bug fixes
UUIDtoBarcode with the from_type = "file_id" argument now returns the IDs in the proper order when more than one UUID is input.
Update makeGRangesListFromCopyNumber examples with new names from API e.g., ‘associated_entities.entity_submitter_id’
Changes in version 1.12.0
New features
makeSummarizedExperimentFromGISTIC has been moved to RTCGAToolbox.
splitAssays now deprecated for TCGAsplitAssays to avoid conflict with MultiAssayExperiment::splitAssays
Minor changes and bug fixes
Properly identifies genome annotation (hg*) in oncoPrintTCGA
qreduceTCGA now works with updates to seqlevelsStyle where genome annotation include patch versions when available
Changes in version 1.10.0
New features
correctBuild attempts to provide the official name of a particular human genome build to agree with changes in GenomeInfoDb
isCorrect checks that the build name matches the official name
Minor changes and bug fixes
Documentation improvements to simplifyTCGA
Improvements to findGRangesCols to locate ranged columns in a DataFrame
Fixed a bug in UUIDtoBarcode where only the first record was returned (#26 , 1)
Fixed a bug in filenameToBarcode when multiple inputs were used (#22 ,
Changes in version 1.8.0
New features
README.md now includes a cheat sheet for reference
mergeColData and oncoPrintTCGA sections updated/included in the vignette
Minor changes and bug fixes
translateBuild more robust to consistent inputs
translateBuild returns vector output instead of single string as before
makeSummarizedExperimentFromGISTIC now has a more open interface with ... input to RTCGAToolbox::getGISTICPeaks
oncoPrintTCGA now uses seqlevels from input throughout
Changes in version 1.6.0
New features
oncoPrintTCGA: Create an oncoPrint visualization for mutation data
Support aliquot_ids as input to UUIDtoBarcode function
Additional sections in the vignette: CpGtoRanges, UUIDtoBarcode for aliquot_ids
TCGAprimaryTumors allows users to select all primary tumors for a given curatedTCGAData MultiAssayExperiment object (suggested by @vjcitn )
Minor changes and bug fixes
Now merging clinical data using both rows and columns in mergeColData
Added informative error when query results are empty in UUIDtoBarcode
Updates to makeGRangesListFromExonFiles to use S4Vectors::splitAsList
Changes in version 1.4.0
New features
trimColData added to remove any extra columns from the colData slot (thanks to @vjcitn )
CpGtoRanges translates CpG islands to genomic positions using an annotation package and minfi
Overhaul of the barcode translation services allows accurate translation of identifiers
splitAssays now separates all assays by sample codes contained therein by default, previous behavior had default values
Documentation for simplifyTCGA was modified to include similar operations, such as, symbolsToRanges, mirToRanges, CpGtoRanges, etc.
Vignette includes comprehensive examples of new functionality
Minor changes and bug fixes
getFileNames renamed to getFileName
TCGAsampleSelect now allows multiple sample type inputs as the sampleCodes argument
getSubtypeMap updates column names to accurately represent patient identifiers
More robust checks were added to splitAssays to ensure valid sample codes in the input and provided as arguments
makeGRangesListFromExonFiles is optimized to use dplyr when available and fast operations from IRanges
Various enhancements to *toRanges functions, including re-using underlying common helper function
The internal weightedmean function in qreduceTCGA has been updated for correctness
The keep arugment in qreduceTCGA and related functions was changed to keep.assay
Changes in version 1.2.0
New features
imputeAssay added to impute data for MultiAssayExperiment assays
UUIDtoUUID translation available to translate from file to case IDs
A suite of functions is available to enhance existing MultiAssayExperiment datasets: qreduceTCGA, mirToRanges, symbolsToRanges. Thanks to @lwaldron
Minor changes and bug fixes
Various changes to examples for compatibility with RaggedExperiment
Bug fix to internal functions for finding GRanges columns
Changes in version 1.1.5
uniformBuilds cleans up a vector of inconsistently labelled builds by changing the build with the lowest frequency
Changes in version 1.1.4
New features
The UUIDtoUUID function can translate from case to file UUIDs and vice versa
imputeAssay allows missing data imputation using KNN for MultiAssayExperiment assays
Changes in version 1.1.1
New features
exported the internal helper, filenameToBarcode. See examples
Changes in version 0.99.68
Minor changes and bug fixes
Minor changes in response to review, avoid switching from logical to numeric index, updated vignette introduction
Fix examples to updated GenomicDataCommons interface
Move RTCGAToolbox to Suggests field in DESCRIPTION
Removed BiocFileCache from Imports field
Changes in version 0.99.51
New features
Added a group of ID translation helper functions (see ?ID-translation)
Added a group of helper functions that work with curatedTCGAData
UUIDtoBarcode function added thanks to @seandavi
Renamed makeGRangesListFromTCGA to makeGRangesListFromCopyNumber
makeSummarizedExperimentFromGISTIC is now available to convert RTCGAToolbox’s FirehoseGISTIC data class to SummarizedExperiment
Created a function to merge external colData to a MultiAssayExperiment colData slot
Revamped vignette documentation
Minor changes and bug fixes
Improvements to TCGAbiospec and TCGAbarcode
Updated sampleTypes and clinicalNames datasets
Updated DESCRIPTION file with appropriate imports and exports
Various improvements to findGRangesCols
generateMap is now updated to the recent MultiAssayExperiment API with improved example
Updated getFileNames to most recent RTCGAToolbox API
Various updates to data generating scripts in data-raw folder
Format updates to NEWS file
Added tests
Changes in version 0.2.0
New features
Package renamed to TCGAutils for working with TCGA data
Changes in version 0.1.0
New features
TCGAtranslateID now works with GDC API
Minor changes and bug fixes
Code cleaned up
Added proper import directives
Changes in version 0.0.70
New features
makeGRangesListFromDataFrame now moved to GenomicRanges
makeSummarizedExperimentFromDataFrame now moved to SummarizedExperiment
getFileNames function will obtain filenames used in RTCGAToolbox
Improved getFileNames with xml2 and rvest dependencies and removes the XML dependency
Minor changes and bug fixes
TCGAextract now uses the findGRangesCols to automatically detect ranged data columns
Arguments in functions TCGA* now renamed to match MultiAssayExperiment conventions
Informative errors in TCGAextract
Changes in version 0.0.60
makeGRangesListFromTCGA data builds on makeGRangesListFromDataFrame
makeGRangesListFromDataFrame and makeRangedSummarizedExperimentFromDataFrame will be moving to standard Bioconductor packages soon.
tcga and ccle functions soon to be deprecated.
Upcoming: TCGAbarcode will be modified for efficiency
Changes in version 0.0.50
Add your own identifier parsing function for generating a sampleMap in generateMap!
Add proper genome build to ranged based objects.
Return SummarizedExperiment class for certain data types.
Fix genome build bugs
Changes in version 0.0.46
makeRSE function for creating a RangedSummarizedExperiment object from a data frame.
Bug fixes to getRangeNames including the option to enter a regular expression vector for finding ranged column names.
matchClinical renamed to TCGAmatchClinical
Changes in version 0.0.44
getRangedNames function will try to extract minimum necessary names for creating ranges (works on a vector of names)
minor bug fixes to TCGAbiospec, TCGAextract, makeGRangesList
Changes in version 0.0.40
Package renamed to BiocInterfaces!
TCGA specific functions now start with the letters TCGA
Included: more examples of use of the TCGAbarcode function
Updated makeGRangesList function to work with tcga and ccle data parameter functions
Changes in version 0.0.2
Added a NEWS.md file to track changes to the package.
TCGAmisc now a standalone package! (previously in RTCGAToolbox)
Provides helper functions for converting raw data into S4 objects (e.g., GRangesList)
Provides functions for creating a MultiAssayExperiment object such as:
generateTCGAmapcleanExpList