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Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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update example to new field values in files() #102

Closed LiNk-NY closed 2 years ago

LiNk-NY commented 2 years ago

Hi Sean, @seandavi Due to changes in the data release, the current OncoPrint query is no longer working. Here is a PR with updates. I wasn't sure if this is the right analysis.workflow_type but it gave me some results:

fnames <- files() %>%
  GenomicDataCommons::filter(
    cases.project.project_id=='TCGA-SKCM' &
      data_format=='maf' &
      data_type=='Masked Somatic Mutation' &
      analysis.workflow_type ==
        'Aliquot Ensemble Somatic Variant Merging and Masking'
  ) %>%
  results(size = 6) %>%
    ids() %>% 
      gdcdata()

Best, Marcel

LiNk-NY commented 2 years ago

This should close #101