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GenomicDataCommons

Build Status

Provide R access to the NCI Genomic Data Commons portal. Some additional detail from the API Users Guide documentation may help.

This package is under development.

QuickStart

library(GenomicDataCommons)
endpoints()            # what can you do? See help page for each endpoint
status()               # is the service up?
experiments(size=100)  # available experiments
lst = cases()          # first 10 cases
lst
lst[1]
lst[[1]]
lst <-                 # submitter_id, sorted descending order
    cases(fields="submitter_id", sort="submitter_id:desc")
lst
sapply(lst, "[[", "submitter_id")

Accessing restricted data requires an authentication token. This in turn requires eRA and dbGAP access. Provide the token as a character string (or, for manifest(), a file path).

slicing("df80679e-c4d3-487b-934c-fcc782e5d46e", symbols=c("BRCA1", "BRCA2"),
        token=token)

See vignette for more details.

TODO

  • manifest() endpoint
  • transfer(): download manifest files via GDC Data Transfer Tool
  • Authentication
  • slicing() endpoint
  • filters implemented using R expression syntax
  • gdcdata() (data endpoint) download md5sums validation
  • validate slicing 'regions' argument
  • Rename as 'gdc' -- accessing gdc portal, without Bioconductor dependencies
  • Develop GenomicDataCommons -- Bioconductor API supporting GenomicRanges, GenomicAlignments, VariantAnnotation.

WON'T DO

  • implement submission