Changelog • curatedTCGAData

Changes in version 1.24.0

Create an on-the-fly sampleMap for RNASeq2GeneNorm* data version 2.1.1. Data source has munged colnames and sample maps were not updated in the latest upload (#59, @LiNk-NY)

Data version 2.1.1 is now availble. It contains updates to RNASeq2GeneNorm*, and RNASeq2Gene*, as well as fixes to the curated subtypes in the colData for OV and SKCM.

When the assays argument was RNASeq2Gene, curatedTCGAData would incorrectly include RNASeq2GeneNorm assays. Users who want to return both assay types should enter RNASeq2Gene* instead (with an asterisk).
When more than one BiocVersion in the metadata was available, the curatedTCGAData function would return duplicate results. This has been fixed to obtain either the matching BiocVersion or the latest version in the metadata.

The version argument now allows users to select either 1.1.38 or 2.0.1.
Version 2.0.1 includes RNASeq2Gene data as RSEM TPM gene expression values (#38, @mherberg).
Genomic information updated for RaggedExperiment type data objects where ‘37’ is now ‘GRCh37’ (#40, @vjcitn).
Datasets (e.g., OV, GBM) that contain multiple assays that could be merged are now provided as merged assays (#27, @lwaldron).
The vignette now includes sections on how to use the TCGAprimaryTumors and getWithColData functions.

mRNAArray assays now return matrix type data instead of DataFrame (#31, @lgeistlinger, @vjcitn).
Removed force download of GISTIC resources
Published article now available with citation("curatedTCGAData")

Output dataset options as table when dry.run is enabled in the main function.
Check for RaggedExperiment dependency when loading data that uses the data representation (@vjcitn, #39)

Control verbosity of curatedTCGAData function with the verbose argument (@lgeistlinger, #35)
Fallback added for when ExperimentHub service is offline (@vjcitn, #36)
Data export section added to main vignette due to new features in MultiAssayExperiment

Add a caveats section for working with TCGA data in the vignette (@vjcitn suggest)
Provide examples for TCGAutils::TCGAsampleSelect in the vignette

Methylation data represented as a DelayedMatrix with associated HDF5 files within a SummarizedExperiment object. They can be downloaded using the Methyl* assay keyword.
Big changes to documentation with table added for detailing ExperimentList data types (thanks to @lgeistlinger)
Vignette now includes some helper functions provided by TCGAutils

TCGAutils is available for use with curatedTCGAData
‘GISTIC_Peak’ datasets are force downloaded due to caching mechanism issues
Issue of missing ‘GISTIC’ data for LAML and SKCM due to incorrect file links has been resolved (#29 @pcheng84)
Updated data documentation