NEWS.md

In TCGAutils: TCGA utility functions for data management

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

TCGAutils documentation built on April 17, 2021, 6:04 p.m.