S3 generic to set GDCQuery fields

Usage

select(x, fields)

# S3 method for class '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] "HCMI-CMDC" "TCGA-KIRC" "CTSP-DLBCL1" "TCGA-BRCA" ...
#>   ..$ dbgap_accession_number: chr [1:10] NA NA "phs001184" NA ...
#>   ..$ project_id            : chr [1:10] "HCMI-CMDC" "TCGA-KIRC" "CTSP-DLBCL1" "TCGA-BRCA" ...
#>   ..$ disease_type          :List of 10
#>   .. ..$ HCMI-CMDC  : chr [1:16] "Soft Tissue Tumors and Sarcomas, NOS" "Complex Mixed and Stromal Neoplasms" "Acinar Cell Neoplasms" "Squamous Cell Neoplasms" ...
#>   .. ..$ TCGA-KIRC  : chr "Adenomas and Adenocarcinomas"
#>   .. ..$ CTSP-DLBCL1: chr "Mature B-Cell Lymphomas"
#>   .. ..$ TCGA-BRCA  : chr [1:9] "Epithelial Neoplasms, NOS" "Adnexal and Skin Appendage Neoplasms" "Squamous Cell Neoplasms" "Adenomas and Adenocarcinomas" ...
#>   .. ..$ MP2PRT-WT  : chr "Neoplasms, NOS"
#>   .. ..$ CPTAC-3    : chr [1:11] "Squamous Cell Neoplasms" "Gliomas" "Adenomas and Adenocarcinomas" "Epithelial Neoplasms, NOS" ...
#>   .. ..$ MATCH-P    : chr [1:10] "Transitional Cell Papillomas and Carcinomas" "Complex Mixed and Stromal Neoplasms" "Mesothelial Neoplasms" "Ductal and Lobular Neoplasms" ...
#>   .. ..$ MATCH-W    : chr [1:8] "Adenomas and Adenocarcinomas" "Ductal and Lobular Neoplasms" "Epithelial Neoplasms, NOS" "Neoplasms, NOS" ...
#>   .. ..$ MATCH-Z1D  : chr [1:8] "Complex Mixed and Stromal Neoplasms" "Myomatous Neoplasms" "Ductal and Lobular Neoplasms" "Neoplasms, NOS" ...
#>   .. ..$ MATCH-Z1A  : chr [1:6] "Adenomas and Adenocarcinomas" "Mesothelial Neoplasms" "Epithelial Neoplasms, NOS" "Neoplasms, NOS" ...
#>  $ query       :List of 4
#>   ..$ fields : chr [1:3] "project_id" "dbgap_accession_number" "disease_type"
#>   ..$ filters: NULL
#>   ..$ facets : NULL
#>   ..$ expand : NULL
#>   ..- attr(*, "class")= chr [1:3] "gdc_projects" "GDCQuery" "list"
#>  $ pages       :List of 7
#>   ..$ count: int 10
#>   ..$ total: int 86
#>   ..$ size : int 10
#>   ..$ from : int 0
#>   ..$ sort : chr ""
#>   ..$ page : int 1
#>   ..$ pages: int 9
#>  $ aggregations: list()
#>  - attr(*, "class")= chr [1:3] "GDCprojectsResponse" "GDCResponse" "list"