NEWS.md

In mksamur/RTCGAToolbox: A new tool for exporting TCGA Firehose data

Changes in version 2.34.0

Significant user-visible changes

• getReport has been removed from the package.

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

Changes in version 2.7.21

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

mksamur/RTCGAToolbox documentation built on Oct. 29, 2023, 10:06 p.m.