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Start a query of GDC metadata

Source: R/query.R
query.Rd

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 facet 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_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 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()