NEWS.md

In waldronlab/TCGAutils: TCGA utility functions for data management

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.

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

waldronlab/TCGAutils documentation built on Feb. 25, 2024, midnight