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