query {GenomicDataCommons} | R Documentation |
The basis for all functionality in this package starts with constructing a query in R. The GDCQuery object contains the filters, facets, and other parameters that define the returned results. A token is required for accessing certain datasets.
query(entity, filters = NULL, facets = NULL, legacy = FALSE, expand = NULL, fields = default_fields(entity)) cases(...) files(...) projects(...) annotations(...)
entity |
character vector of 'cases','files','annotations', or 'projects' |
filters |
a filter list, typically created using |
facets |
a character vector of |
legacy |
logical(1) whether to use the "legacy" archive or not. See https://docs.gdc.cancer.gov/Data_Portal/Users_Guide/Legacy_Archive/ and https://gdc-portal.nci.nih.gov/legacy-archive/search/f for details. |
expand |
a character vector of "expands" to include in returned data |
fields |
a character vector of fields to return |
... |
passed through to |
An S3 object, the GDCQuery object. This is a list with the following members.
filters
facets
fields
expand
archive
token
cases
: convenience contructor for a GDCQuery for cases
files
: convenience contructor for a GDCQuery for cases
projects
: convenience contructor for a GDCQuery for cases
annotations
: convenience contructor for a GDCQuery for annotations
qcases = query('cases') # equivalent to: qcases = cases()