NEWS

RTCGAToolbox 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.

RTCGAToolbox 2.32.0

New features

The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been removed from the package.

RTCGAToolbox 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.

RTCGAToolbox 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 <gdac.broadinstitute.org> (@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.

RTCGAToolbox 2.24.0

Bug fixes and minor improvements

The deprecated functionality vignette moved to the vignettes/analysis/ folder

RTCGAToolbox 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

RTCGAToolbox 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

RTCGAToolbox 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

RTCGAToolbox 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)

RTCGAToolbox 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

RTCGAToolbox 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

RTCGAToolbox 2.9.41

Bug fixes and minor improvements

Fixed bug where file rename was not working due to incorrect path location in getFirehoseData

RTCGAToolbox 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

RTCGAToolbox 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

RTCGAToolbox 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