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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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Order of argument `assays` and resulting ExperimentList #25

Open lgeistlinger opened 5 years ago

lgeistlinger commented 5 years ago 
> gbm <- curatedTCGAData("GBM", c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"), FALSE)
> gbm
A MultiAssayExperiment object of 3 listed
 experiments with user-defined names and respective classes. 
 Containing an ExperimentList class object of length 3: 
 [1] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns 
 [2] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns 
 [3] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns 
Features: 
 experiments() - obtain the ExperimentList instance 
 colData() - the primary/phenotype DataFrame 
 sampleMap() - the sample availability DataFrame 
 `$`, `[`, `[[` - extract colData columns, subset, or experiment 
 *Format() - convert into a long or wide DataFrame 
 assays() - convert ExperimentList to a SimpleList of matrices

How difficult would it actually be for the resulting MAE to have its ExperimentList in the order of the input assays argument of curatedTCGAData? I think this would be more intuitive.