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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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unmerged datasets #9

Closed lwaldron closed 6 years ago

lwaldron commented 6 years ago

I haven't checked all the cancer types; this would be a good unit test (make sure that the returned data types are within the expected types for each cancer). See GBM_CNACGH1, GBM_CNACGH2, GBM_Methylation1, GBM_Methylation2:

> curatedTCGAData("GBM", "*")
                                 GBM_CNACGH1                                  GBM_CNACGH2 
       "GBM_CNACGH_CGH_hg_244a-20160128.rda" "GBM_CNACGH_CGH_hg_415k_g4124a-20160128.rda" 
                                  GBM_CNASNP                                   GBM_CNVSNP 
                   "GBM_CNASNP-20160128.rda"                    "GBM_CNVSNP-20160128.rda" 
                        GBM_GISTIC_AllByGene                 GBM_GISTIC_ThresholdedByGene 
         "GBM_GISTIC_AllByGene-20160128.rda"  "GBM_GISTIC_ThresholdedByGene-20160128.rda" 
                            GBM_Methylation1                             GBM_Methylation2 
     "GBM_Methylation_methyl27-20160128.rda"     "GBM_Methylation_methyl450-20160128.rda" 
                            GBM_miRNASeqGene                                 GBM_Mutation 
             "GBM_miRNASeqGene-20160128.rda"                  "GBM_Mutation-20160128.rda" 
                         GBM_RNASeq2GeneNorm                                GBM_RPPAArray 
          "GBM_RNASeq2GeneNorm-20160128.rda"                 "GBM_RPPAArray-20160128.rda" 
>
LiNk-NY commented 6 years ago

@lwaldron These are not merged because they do not match in either features or columns. These are left as is. In cases where they do match, they are merged.

There are a few datasets that are missing from the results. I will fix this in a forthcoming commit.

Thanks, Marcel

LiNk-NY commented 6 years ago

Changes in 981598d249fb770dc1a751ae9778dbe2f5afeaee

LiNk-NY commented 6 years ago

These are different platforms and can't be merged. We want to provide the data for all available platforms from RTCGAToolbox. I'm closing the issue for now.