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waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data
https://waldronlab.io/MultiAssayExperiment/
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Fix pradMAEO-RTCGAToolbox vignette #201

Closed lawremi closed 7 years ago

lawremi commented 7 years ago

That vignette still claims that RTCGAToolbox is from GitHub, but it's now on Bioconductor. It looks like you are using readr for type_convert() but maybe you could instead just use utils::type.convert(). The function buildMultiAssayExperiments() seems broken because the variable TCGAcodes does not exist in the frame of the function (by my eye). Maybe co should be cancerObject? It should probably be put into some package, ideally RTCGAToolbox, which IMO should be giving us MAE's directly. Please also look into using BiocFileCache.

From reading the vignette, I learned that there are many opportunities for improving how we access TCGA from Bioconductor, but that's another story.

lwaldron commented 7 years ago

Sorry about that - the risks of an unevaluated vignette. @schifferl I fixed a couple errors and got rid of the readr dependency, see changes. @lawremi , the dependency on BiocInstaller::biocLite("LiNk-NY/RTCGAToolbox") is necessary, as this version added an extract function to generate basic Bioconductor objects (GRangesList, ExpressionSet, SummarizedExperiment), that the RTCGAToolbox maintainer hasn't incorporated.

This vignette should soon be deprecated by curatedTCGAData::curatedTCGAData().