Per-assay sample counts for a cohort

Summarizes how many samples each subject has for each assay. This is the table most studies ask for first: which subjects are missing which assay.

Usage

completeness(cohort, wide = FALSE)

Arguments

cohort

A Cohort object.

wide

Logical. When FALSE (default), returns one row per subject_id x assay with an n_samples count. When TRUE, pivots to one row per subject and one column per assay, with 0 where a subject has no sample for that assay.

Value

A tibble. See wide above for its shape.

Details

The wide form always has one row per subject in cohort@subject_tbl, even a subject with zero samples for every assay, and one column per assay that appears anywhere in cohort@sample_map.

See also

subjects(), samples(), validate_manifest()

Examples

data(example_cohort)
completeness(example_cohort)
#> # A tibble: 8 × 3
#>   subject_id assay n_samples
#>   <chr>      <chr>     <int>
#> 1 MOUSE001   scrna         1
#> 2 MOUSE001   wes           2
#> 3 MOUSE002   scrna         1
#> 4 MOUSE002   wes           2
#> 5 RAT001     scrna         1
#> 6 RAT001     wes           2
#> 7 RAT002     scrna         1
#> 8 RAT002     wes           2
completeness(example_cohort, wide = TRUE)
#> # A tibble: 4 × 3
#>   subject_id scrna   wes
#>   <chr>      <int> <int>
#> 1 MOUSE001       1     2
#> 2 MOUSE002       1     2
#> 3 RAT001         1     2
#> 4 RAT002         1     2