query {GenomicDataCommons} | R Documentation

## 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(...)

    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()

[Package GenomicDataCommons version 1.18.0 Index]