getReporthas been removed from the package.
- Remove unnecessary imports e.g., from
RCircos.
- The functions
getCNGECorrelation,getDiffExpressedGenes, andgetSurvivalhave been removed from the package.
- Include additional options for
miRNASeqGeneTypeandRNAseq2Norminputs, see?getFirehoseData. - The functions
getCNGECorrelation,getDiffExpressedGenes, andgetSurvivalhave been defunct and will be removed from the package (see?'RTCGAToolbox-defunct'). - The
RNAseq2Normargument ingetFirehoseDataallows additional options: "RSEM_normalized_log2", "raw_counts", "scaled_estimate" from the 'preprocessed' tarballs in Firehose. The "normalized_counts" default remains.
getFirehoseDatawhen used with themiRNASeqGeneargument was downloading read counts data rather than RPM. This has been fixed with themiRNASeqGeneTypeargument. "read_count" and "cross-mapped" data are still available but must be entered explicitly inmiRNASeqGeneType.
- 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
makeSummarizedExperimentFromGISTICinterface withrownameColinput, type checking, and set row names when the are not duplicated.
- 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 withSummarizedExperiment.
- The deprecated functionality vignette moved to the
vignettes/analysis/folder
makeSummarizedExperimentFromGISTICtransferred fromTCGAutils
biocExtractnow merges datasets from the same platforms- Re-worked and simplified
getDatamethod forFirehoseDataandFirehoseGISTIC - Remove missing ranges when creating
GRangesandGRangesListfromDataFrame
- Added the
RNASeq2Geneslot to theFirehoseDataclass. This data type mainly obtains RNASeq v2raw_countsfrom the pipeline (scaled_estimatesalso available; @mherberg #39) - Added an
accminiexample dataset as obtained fromgetFirehoseData getLinksfunction shows the user some file provenance based on data requested- Newly deprecated functions:
getDiffExpressedGenes,getCNGECorrelation,getSurvivalandgetReport. 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.
- Improvements to internal functions for converting tabular data to Bioconductor classes
- Missing (NA)
seqnamesare removed when converting toRaggedExperiment - Remove static file dependencies from GitHub and use text inside function (@DavisWeaver, #34)
- Added default values to helper for making
SummarizedExperimentdatasets - Coerce sample names to character when in (the rare) case they're numeric
- Added an ellipsis argument to
biocExtractfor specifying thenames.fieldin tabular data that will correspond to the row names of aSummarizedExperiment
- Warning for Windows users added when file paths are too long
getGISTICPeaksnow requires aFirehoseGISTICdata object obtained fromgetFirehoseData
- Consolidate GISTIC data download methods in
getFirehoseDataandgetGISTICPeaks - Increase robustness of internal helper functions that work with strands
- 'TCGA' sample column identification is less strict
RNASeq2GeneNormslot in theFirehoseDataclass is alistnow (frommatrix)- Use
tempdir()as the default directory for downloading data ingetFirehoseData
- Save all
RNASeq2GeneNormdatasets 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
httrinstead of 'canevolve.org' query (@mksamur, #32)
- GISTIC data for
SKCMandLAMLis correctly returned by thegetFirehoseDatafunction - Helpers now correctly assign row names in presence of ranged data when
using
biocExtract
biocExtractcan now return GISTIC peak data as well with the 'GISTICP' option- Methylation data is now converted to
DelayedArrayand contained inSummarizedExperimentobjects viabiocExtract - Added an
isEmptymethod to theFirehoseGISTICdata class
- Set default 'peak' argument to 'wide'
- Functionality from the
TCGAutilspackage is now employed such asfindGRangesColsanduniformBuilds
- Fixed bug where file rename was not working due to incorrect path location
in
getFirehoseData
getBroadSubtypesandgetGISTICPeaksnow included in the package. Thanks to @lgeistlinger!- Updated import directives
- Added peaks data slot to the
FirehoseGISTICclass - Numerous improvements to internal helpers
- Added a
GISTICargument togetFirehoseData
selectTypefunction replaces all previous data type extractor functionsgetDataimproved, removedCNargument- Cleaner documentation for
biocExtract
- Included helper functions for enabling full functionality of
biocExtract - Added appropriate import directives
- Re-organized documentation for readability
biocExtractfunction now available - convert data objects to Bioconductor friendly data classes
- New maintainer for package
- Updated API - see
FirehoseDataslots for changes - New extractor functions for slots of
FirehoseData - Standardize argument names and slots
- Export functions in package
- Updated NAMESPACE
- Cleaner documentation
- Import directives appropriate
- Example dataset updated to new API