S3 generic to set GDCQuery fields

Usage

select(x, fields)

# S3 method for GDCQuery
select(x, fields)

Arguments

x: the objects on which to set fields
fields: a character vector specifying the fields

Value

A GDCQuery object, with the fields member altered.

Methods (by class)

select(GDCQuery): set fields on a GDCQuery object

Examples

gProj = projects()
gProj$fields
#>  [1] "dbgap_accession_number" "disease_type"           "intended_release_date" 
#>  [4] "name"                   "primary_site"           "project_autocomplete"  
#>  [7] "project_id"             "releasable"             "released"              
#> [10] "state"                 
head(available_fields(gProj))
#> [1] "dbgap_accession_number"         "disease_type"                  
#> [3] "intended_release_date"          "name"                          
#> [5] "primary_site"                   "program.dbgap_accession_number"
default_fields(gProj)
#>  [1] "dbgap_accession_number" "disease_type"           "intended_release_date" 
#>  [4] "name"                   "primary_site"           "project_autocomplete"  
#>  [7] "project_id"             "releasable"             "released"              
#> [10] "state"                 

gProj %>%
  select(default_fields(gProj)[1:2]) %>%
  response() %>%
  str(max_level=2)
#> List of 4
#>  $ results     :'data.frame':	10 obs. of  4 variables:
#>   ..$ id                    : chr [1:10] "TARGET-NBL" "GENIE-GRCC" "GENIE-DFCI" "GENIE-NKI" ...
#>   ..$ dbgap_accession_number: chr [1:10] "phs000467" NA NA NA ...
#>   ..$ project_id            : chr [1:10] "TARGET-NBL" "GENIE-GRCC" "GENIE-DFCI" "GENIE-NKI" ...
#>   ..$ disease_type          :List of 10
#>   .. ..$ TARGET-NBL: chr [1:2] "Neuroepitheliomatous Neoplasms" "Not Applicable"
#>   .. ..$ GENIE-GRCC: chr [1:32] "Osseous and Chondromatous Neoplasms" "Synovial-like Neoplasms" "Fibromatous Neoplasms" "Myomatous Neoplasms" ...
#>   .. ..$ GENIE-DFCI: chr [1:52] "Osseous and Chondromatous Neoplasms" "Other Leukemias" "Synovial-like Neoplasms" "Lymphoid Leukemias" ...
#>   .. ..$ GENIE-NKI : chr [1:23] "Synovial-like Neoplasms" "Fibromatous Neoplasms" "Myomatous Neoplasms" "Transitional Cell Papillomas and Carcinomas" ...
#>   .. ..$ GENIE-VICC: chr [1:43] "Neoplasms, NOS" "Adnexal and Skin Appendage Neoplasms" "Squamous Cell Neoplasms" "Gliomas" ...
#>   .. ..$ GENIE-UHN : chr [1:39] "Other Leukemias" "Osseous and Chondromatous Neoplasms" "Synovial-like Neoplasms" "Lymphoid Leukemias" ...
#>   .. ..$ GENIE-MDA : chr [1:34] "Osseous and Chondromatous Neoplasms" "Synovial-like Neoplasms" "Fibromatous Neoplasms" "Myomatous Neoplasms" ...
#>   .. ..$ GENIE-MSK : chr [1:49] "Osseous and Chondromatous Neoplasms" "Synovial-like Neoplasms" "Lymphoid Leukemias" "Fibromatous Neoplasms" ...
#>   .. ..$ GENIE-JHU : chr [1:33] "Osseous and Chondromatous Neoplasms" "Other Leukemias" "Synovial-like Neoplasms" "Lymphoid Leukemias" ...
#>   .. ..$ FM-AD     : chr [1:23] "Gliomas" "Acinar Cell Neoplasms" "Specialized Gonadal Neoplasms" "Miscellaneous Tumors" ...
#>  $ query       :List of 5
#>   ..$ fields : chr [1:3] "project_id" "dbgap_accession_number" "disease_type"
#>   ..$ filters: NULL
#>   ..$ facets : NULL
#>   ..$ legacy : logi FALSE
#>   ..$ expand : NULL
#>   ..- attr(*, "class")= chr [1:3] "gdc_projects" "GDCQuery" "list"
#>  $ pages       :List of 7
#>   ..$ count: int 10
#>   ..$ total: int 72
#>   ..$ size : int 10
#>   ..$ from : int 0
#>   ..$ sort : chr ""
#>   ..$ page : int 1
#>   ..$ pages: int 8
#>  $ aggregations: list()
#>  - attr(*, "class")= chr [1:3] "GDCprojectsResponse" "GDCResponse" "list"