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.
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
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Additional details are provided on the HuBMAP consortium webpage, https://software.docs.hubmapconsortium.org/apis
Examples
donors()
#> # A tibble: 239 × 8
#> uuid hubmap_id group_name Sex Age `Body Mass Index` Race
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 03b82562be364ef0301… HBM232.Q… Universit… Male 11 NA Blac…
#> 2 c09f875545a64694d70… HBM534.P… TTD - Uni… Fema… 90 NA White
#> 3 0abacde2443881351ff… HBM358.K… TTD - Uni… Male 90 NA White
#> 4 d7c90f1fe1ae702df84… HBM639.M… TTD - Uni… Fema… 59 NA White
#> 5 b1acd1731563347de3a… HBM674.F… TTD - Uni… Fema… 60 NA White
#> 6 24e6946400b65468a96… HBM379.B… TTD - Uni… Male 79 NA White
#> 7 c9c39035edc9de812f6… HBM543.J… TTD - Uni… Male 71 NA White
#> 8 f079501ef0915131c8b… HBM448.V… TTD - Uni… Fema… 82 NA White
#> 9 a0bea4ae0ce4e03efd0… HBM666.X… TTD - Uni… Fema… 82 NA White
#> 10 03b6236566cfd447214… HBM263.S… TTD - Uni… Fema… 75 NA White
#> # ℹ 229 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 × 24
#> 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 20 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>, lab_donor_id <chr>,
#> # label <chr>, last_modified_timestamp <dbl>, metadata <list>,
#> # protocol_url <chr>, submission_id <chr>, uuid <chr>
uuid <- "1dcde05aea3509b2cf89a41ceb3d700f"
donor_derived(uuid, "Sample")
#> # A tibble: 17 × 3
#> uuid organ derived_dataset_count
#> <chr> <chr> <int>
#> 1 146c221bca3759ffa64cd01bc7069cf3 Kidney (Right) 12
#> 2 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 3 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 4 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 5 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 6 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 7 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 8 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 9 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 10 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 11 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 12 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 13 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 14 27485b21a2285dbcae38f2d56d429dec Kidney (Right) 12
#> 15 1441346ca08aadbb631539663ab1874a Kidney (Right) 2
#> 16 e97fd3e2b6dae2238cfe052a91409f40 Kidney (Right) 2
#> 17 92cd878bf5be78131c6a3f701342a3ac Kidney (Right) 8
uuid <- "d37df2cad4e80dc368763caefccf7140"
donor_metadata(uuid)
#> # A tibble: 8 × 2
#> Key Value
#> <chr> <chr>
#> 1 Age "49 year"
#> 2 Body Mass Index "31.2 kg/m2"
#> 3 Cause of Death "Gunshot wound "
#> 4 Death Event "Suicide "
#> 5 Height "72 inches"
#> 6 Race "White "
#> 7 Sex "Male "
#> 8 Weight "230 pounds"