Order of argument `assays` and resulting ExperimentList
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lgeistlinger commented
> 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.