query: Start a query of GDC metadata

In GenomicDataCommons: NIH / NCI Genomic Data Commons Access

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(...)

ssms(...)

ssm_occurrences(...)

cnvs(...)

cnv_occurrences(...)

genes(...)

Arguments

entity	character vector, including one of the entities in .gdc_entities
filters	a filter list, typically created using make_filter, or added to an existing GDCQuery object using filter.
facets	a character vector of facets for counting common values. See available_fields. In general, one will not specify this parameter but will use facets instead.
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. See available_expands
fields	a character vector of fields to return. See available_fields. In general, one will not specify fields directly, but instead use select
...	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 files

• projects: convenience contructor for a GDCQuery for projects

• annotations: convenience contructor for a GDCQuery for annotations

• ssms: convenience contructor for a GDCQuery for ssms

• ssm_occurrences: convenience contructor for a GDCQuery for ssm_occurrences

• cnvs: convenience contructor for a GDCQuery for cnvs

• cnv_occurrences: convenience contructor for a GDCQuery for cnv_occurrences

• genes: convenience contructor for a GDCQuery for genes

Examples

qcases = query('cases')
# equivalent to:
qcases = cases()

GenomicDataCommons documentation built on Nov. 8, 2020, 11:08 p.m.