Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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.gdc_list print output might be a bit misleading #18

Closed seandavi closed 7 years ago

seandavi commented 7 years ago

Below, the files_list returned shows cases(8) which someone might interpret as 8 cases associated with the file. Not sure what the right answer is supposed to be, but in this particular instance, it is ambiguous what "cases" means. Should clarify.

> a = files(fields=grep('case',mapping('files')$fields,value=TRUE)[1:20])
> a[1]
class: files_list
files: 1
names:
    5fc5ee74-3001-4deb-bfdf-b21695128a09
fields:
    cases(8)
> a[1]$`5fc5ee74-3001-4deb-bfdf-b21695128a09`
$cases
                          submitter_id           demographic.updated_datetime 
                        "TCGA-P3-A6T6"     "2016-09-02T18:57:19.863724-05:00" 
                    demographic.gender             demographic.demographic_id 
                                "male" "3dca884d-56d7-5cab-b435-4b64c1986ec9" 
             demographic.year_of_birth                       demographic.race 
                                "1956"                                "white" 
              demographic.submitter_id                       updated_datetime 
            "TCGA-P3-A6T6_demographic"     "2016-09-08T12:09:02.830347-05:00" 
seandavi commented 7 years ago

Will close this and focus efforts on #4.