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waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data
https://waldronlab.io/MultiAssayExperiment/
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Subsequently Reordering a Renamed Experiment List Causes All Samples to be Dropped #320

Closed DarioS closed 1 year ago

DarioS commented 1 year ago

Renaming and reordering

library(curatedTCGAData)
melanoma <- curatedTCGAData(diseaseCode = "SKCM", assays = c("RNASeq2GeneNorm", "miRNASeqGene"), 
                            version = "2.0.1", dry.run = FALSE)
names(melanoma) <- c("mRNA", "miRNA")
melanoma[ , , 2:1]

results in

harmonizing input:
  removing 925 sampleMap rows with 'colname' not in colnames of experiments
  removing 469 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 2 listed
 experiments with user-defined names and respective classes.
 Containing an ExperimentList class object of length 2:
 [1] miRNA: SummarizedExperiment with 20501 rows and 0 columns
 [2] mRNA: SummarizedExperiment with 1046 rows and 0 columns
LiNk-NY commented 1 year ago

Hi Dario, @DarioS Sorry for the late response, I was away. I will take a look at it today. Best, Marcel

LiNk-NY commented 1 year ago

Thanks for reporting. It should be fixed here: 8d031144e4e3d5ab9cf237e1a28c16de141383e7