HuBMAP Donors — donors • HuBMAPR

donors() returns details about available samples, ordered by last modified dates

*_columns() returns a tibble or named character vector describing the content of the tibble returned by samples(), datasets(), donors(), collections(), or publications().

donor_detail() takes a unique donor_id and returns details about one specified sample as a tibble

donor_derived() takes a unique donor_id and returns the derived dataset or/and sample details.

donor_metadata() takes a unique donor_id and returns the metadata of the donor.

Usage

donors()

donors_default_columns(as = c("tibble", "character"))

donor_detail(uuid)

donor_derived(uuid, entity_type = c("Dataset", "Sample"))

donor_metadata(uuid)

Arguments

as: character(1) return format. One of "tibble" (default), or "character".
uuid: character(1) corresponding to the HuBMAP Donor UUID string. This is expected to be a 32-digit hex number.
entity_type: character(1) selected derived entity type. One of "Sample" or "Dataset" (default).

Value

*_columns() returns a named list name containing the column name used in the tibble returned by samples(), datasets(), donors(), collections(), or publications(). When as = "tibble",the return value is a tibble with paths as elements and abbreviations as names.

Details

Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis

Examples

donors()
#> # A tibble: 267 × 8
#>    uuid                 hubmap_id group_name Sex     Age `Body Mass Index` Race 
#>    <chr>                <chr>     <chr>      <chr> <dbl>             <dbl> <chr>
#>  1 e3d3717ad581030c03b… HBM735.B… Universit… Fema…    55              27.5 White
#>  2 dfd0352b60504b32189… HBM825.G… Universit… Fema…    57              30.5 White
#>  3 7525aa868f2f7d2508f… HBM939.T… Universit… Male     56              27.7 Blac…
#>  4 e742ac485a0614e4114… HBM773.M… Universit… Fema…    69              49.2 White
#>  5 80861d1897f0427a91e… HBM296.V… Stanford … Male     37              27.9 White
#>  6 34a06f973f6f62344f1… HBM384.J… TTD - Pen… Fema…    51              NA   White
#>  7 95c77745825d5e47a0c… HBM697.K… TMC - Uni… Male     20              19.4 Unkn…
#>  8 f8667a764f967d780c4… HBM683.T… TMC - Uni… Fema…    34              33.5 White
#>  9 2bc97ff609a8775454b… HBM233.R… TMC - Uni… Fema…    45              35.3 Unkn…
#> 10 c09f875545a64694d70… HBM534.P… TTD - Uni… Fema…    90              NA   White
#> # ℹ 257 more rows
#> # ℹ 1 more variable: last_modified_timestamp <chr>
donors_default_columns()
#> # A tibble: 8 × 1
#>   columns                
#>   <chr>                  
#> 1 hubmap_id              
#> 2 uuid                   
#> 3 group_name             
#> 4 Sex                    
#> 5 Age                    
#> 6 Body Mass Index        
#> 7 Race                   
#> 8 last_modified_timestamp

uuid <- "1dcde05aea3509b2cf89a41ceb3d700f"
donor_detail(uuid)
#> # A tibble: 1 × 21
#>   ancestor_ids ancestors  created_by_user_displayname created_by_user_email     
#>   <list>       <list>     <chr>                       <chr>                     
#> 1 <list [0]>   <list [0]> Jamie Allen                 jamie.l.allen@vanderbilt.…
#> # ℹ 17 more variables: created_timestamp <dbl>, data_access_level <chr>,
#> #   descendant_ids <list>, descendants <list>, description <chr>,
#> #   display_subtype <chr>, entity_type <chr>, group_name <chr>,
#> #   group_uuid <chr>, hubmap_id <chr>, immediate_ancestor_ids <list>,
#> #   immediate_descendant_ids <list>, index_version <chr>,
#> #   last_modified_timestamp <dbl>, metadata <list>, protocol_url <chr>,
#> #   uuid <chr>
uuid <- "1dcde05aea3509b2cf89a41ceb3d700f"
donor_derived(uuid, "Sample")
#> # A tibble: 5 × 3
#>   uuid                             organ          derived_dataset_count
#>   <chr>                            <chr>                          <int>
#> 1 146c221bca3759ffa64cd01bc7069cf3 Kidney (Right)                    12
#> 2 27485b21a2285dbcae38f2d56d429dec Kidney (Right)                    12
#> 3 1441346ca08aadbb631539663ab1874a Kidney (Right)                     2
#> 4 e97fd3e2b6dae2238cfe052a91409f40 Kidney (Right)                     2
#> 5 92cd878bf5be78131c6a3f701342a3ac Kidney (Right)                     8

uuid <- "d37df2cad4e80dc368763caefccf7140"
donor_metadata(uuid)
#> # A tibble: 8 × 2
#>   Key             Value           
#>   <chr>           <chr>           
#> 1 Age             "49.0 years"    
#> 2 Body Mass Index "31.20 kg/m2"   
#> 3 Cause of Death  "Gunshot wound "
#> 4 Death Event     "Suicide "      
#> 5 Height          "182.88 cm"     
#> 6 Race            "White "        
#> 7 Sex             "Male "         
#> 8 Weight          "104.55 kg"