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.
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.
-
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.
- implement submission