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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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OncoPrint section not working in somatic_mutations.Rmd #101

Closed LiNk-NY closed 1 year ago

LiNk-NY commented 2 years ago

Hi Sean, @seandavi

It looks like query in the somatic_mutations.Rmd file would need to get updated to something like: 

fnames = files() %>%
  GenomicDataCommons::filter(
    cases.project.project_id=='TCGA-SKCM' &
      data_format=='MAF' &
      data_type=='Annotated Somatic Mutation' &
      analysis.workflow_type=='MuTect2 Annotation') %>%
  ids() %>%
  gdcdata()

BUT I get an error: 

Error in (function (uri, destination, overwrite, progress, token = NULL, : 
Forbidden (HTTP 403).

Is this accessing restricted data?