Changes in version 2.34.0 Significant user-visible changes - getReport has been removed from the package. Bug fixes and minor improvements - Remove unnecessary imports e.g., from RCircos. Changes in version 2.32.0 New features - The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been removed from the package. Changes in version 2.30.0 New features - Include additional options for miRNASeqGeneType and RNAseq2Norm inputs, see ?getFirehoseData. - The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been defunct and will be removed from the package (see ?'RTCGAToolbox-defunct'). - The RNAseq2Norm argument in getFirehoseData allows additional options: "RSEM_normalized_log2", "raw_counts", "scaled_estimate" from the 'preprocessed' tarballs in Firehose. The "normalized_counts" default remains. Bug fixes and minor improvements - getFirehoseData when used with the miRNASeqGene argument was downloading read counts data rather than RPM. This has been fixed with the miRNASeqGeneType argument. "read_count" and "cross-mapped" data are still available but must be entered explicitly in miRNASeqGeneType. Changes in version 2.28.0 New features - Resolve disparate columns in mutation files from GBMLGG (@andreagrioni, #45) - Update codebase to download https resources from newer layout in (@biostars-nyc, #44). - Update makeSummarizedExperimentFromGISTIC interface with rownameCol input, type checking, and set row names when the are not duplicated. Bug fixes and minor improvements - Use cache directory obtained from tools::R_user_dir - Clean up class membership checks, e.g., with is(x, "classname") - Set missing rows to "" for downstream compatibility with SummarizedExperiment. Changes in version 2.24.0 Bug fixes and minor improvements - The deprecated functionality vignette moved to the vignettes/analysis/ folder Changes in version 2.22.0 New features - makeSummarizedExperimentFromGISTIC transferred from TCGAutils Bug fixes and minor improvements - biocExtract now merges datasets from the same platforms - Re-worked and simplified getData method for FirehoseData and FirehoseGISTIC - Remove missing ranges when creating GRanges and GRangesList from DataFrame Changes in version 2.20.0 New features - Added the RNASeq2Gene slot to the FirehoseData class. This data type mainly obtains RNASeq v2 raw_counts from the pipeline (scaled_estimates also available; @mherberg #39) - Added an accmini example dataset as obtained from getFirehoseData - getLinks function shows the user some file provenance based on data requested - Newly deprecated functions: getDiffExpressedGenes, getCNGECorrelation, getSurvival and getReport. It is no longer possible for the maintainer to update these functions in a way that would benefit users. A transfer of responsibility would be required, i.e. to another package. - Vignettes are updated to reflect changes in the codebase. Bug fixes and minor improvements - Improvements to internal functions for converting tabular data to Bioconductor classes - Missing (NA) seqnames are removed when converting to RaggedExperiment - Remove static file dependencies from GitHub and use text inside function (@DavisWeaver, #34) - Added default values to helper for making SummarizedExperiment datasets - Coerce sample names to character when in (the rare) case they're numeric - Added an ellipsis argument to biocExtract for specifying the names.field in tabular data that will correspond to the row names of a SummarizedExperiment Changes in version 2.18.0 New features - Warning for Windows users added when file paths are too long - getGISTICPeaks now requires a FirehoseGISTIC data object obtained from getFirehoseData Bug fixes and minor improvements - Consolidate GISTIC data download methods in getFirehoseData and getGISTICPeaks - Increase robustness of internal helper functions that work with strands - 'TCGA' sample column identification is less strict Changes in version 2.16.0 New features - RNASeq2GeneNorm slot in the FirehoseData class is a list now (from matrix) - Use tempdir() as the default directory for downloading data in getFirehoseData Bug fixes and minor improvements - Save all RNASeq2GeneNorm datasets within the output object as a list. Previously, only the last dataset would get returned (#30) - Read files from the appropriate download location in getFirehoseData - Move static text file references from 'canevolve.org' to GitHub hosted locations - Check file sizes using httr instead of 'canevolve.org' query (@mksamur, #32) Changes in version 2.14.0 Bug fixes and minor improvements - GISTIC data for SKCM and LAML is correctly returned by the getFirehoseData function - Helpers now correctly assign row names in presence of ranged data when using biocExtract Changes in version 2.12.0 New features - biocExtract can now return GISTIC peak data as well with the 'GISTICP' option - Methylation data is now converted to DelayedArray and contained in SummarizedExperiment objects via biocExtract - Added an isEmpty method to the FirehoseGISTIC data class Bug fixes and minor improvements - Set default 'peak' argument to 'wide' - Functionality from the TCGAutils package is now employed such as findGRangesCols and uniformBuilds Changes in version 2.9.41 Bug fixes and minor improvements - Fixed bug where file rename was not working due to incorrect path location in getFirehoseData Changes in version 2.9.40 New features - getBroadSubtypes and getGISTICPeaks now included in the package. Thanks to @lgeistlinger! - Updated import directives - Added peaks data slot to the FirehoseGISTIC class - Numerous improvements to internal helpers - Added a GISTIC argument to getFirehoseData Changes in version 2.7.44 New features - selectType function replaces all previous data type extractor functions - getData improved, removed CN argument - Cleaner documentation for biocExtract Bug fixes and minor improvements - Included helper functions for enabling full functionality of biocExtract - Added appropriate import directives - Re-organized documentation for readability Changes in version 2.7.21 New features - biocExtract function now available - convert data objects to Bioconductor friendly data classes New features - New maintainer for package - Updated API - see FirehoseData slots for changes - New extractor functions for slots of FirehoseData - Standardize argument names and slots - Export functions in package - Updated NAMESPACE Bug fixes and minor improvements - Cleaner documentation - Import directives appropriate - Example dataset updated to new API