Use an on-the-fly sampleMap from the data to recover munged RNASeq2GeneNorm data

[LiNk-NY]

To reproduce:

curatedTCGAData::curatedTCGAData(c("ACC", "COAD"), "RNASeq2GeneNorm*", version = "2.1.1", dry.run = FALSE)
#> harmonizing input:
#>   removing 6094 sampleMap rows not in names(experiments)
#>   removing 79 sampleMap rows with 'colname' not in colnames of experiments
#>   removing 94 colData rownames not in sampleMap 'primary'
#> A MultiAssayExperiment object of 3 listed
#>  experiments with user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 3:
#>  [1] COAD_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 191 columns
#>  [2] COAD_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 326 columns
#>  [3] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17716 rows and 0 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files

^{Created on 2023-09-12 with reprex v2.0.2}

with fix:

curatedTCGAData::curatedTCGAData(c("ACC", "COAD"), "RNASeq2GeneNorm*", version = "2.1.1", dry.run = FALSE)
#> harmonizing input:
#>   removing 6094 sampleMap rows not in names(experiments)
#>   removing 15 colData rownames not in sampleMap 'primary'
#> A MultiAssayExperiment object of 4 listed
#>  experiments with user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 4:
#>  [1] COAD_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 191 columns
#>  [2] COAD_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 326 columns
#>  [3] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17716 rows and 79 columns
#>  [4] COAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18025 rows and 498 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files

^{Created on 2023-09-12 with reprex v2.0.2}