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