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, @DarioS)
- Fixed a bug in filenameToBarcode when multiple inputs were used
(#22, @DarioS)
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 (@hpages)
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:
- generateTCGAmap
- cleanExpList