query: Start a query of GDC metadata

In Bioconductor/GenomicDataCommons: NIH / NCI Genomic Data Commons Access

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,
  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 facet instead.
expand	a character vector of "expands" to include in returned data. See available_expand
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 constructor 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()

Bioconductor/GenomicDataCommons documentation built on Oct. 31, 2024, 7 a.m.