GenomicDataCommons (version 1.3.4)

query: Start a query of GDC metadata

Description

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.

Usage

query(entity, filters = NULL, facets = NULL, legacy = FALSE,
  expand = NULL, fields = default_fields(entity))
cases(...)
files(...)
projects(...)
annotations(...)

Arguments

entity

character vector of 'cases','files','annotations', or 'projects'

filters

a filter list, typically created using make_filter, or added to an existing GDCQuery object using filter.

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 query

Value

An S3 object, the GDCQuery object. This is a list with the following members.

• filters

• facets

• fields

• expand

• archive

• token

Functions

• 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

Examples

# NOT RUN {
qcases = query('cases')
# equivalent to:
qcases = cases()

# }