Generate Data-Overview Summary

Returns a compact field-coverage overview as an AlphaVarOverview object. The $summary tibble contains one row per tracked field showing the number of unique values, missing values (NA), and empty values (zero-length or whitespace-only strings). A special "entries" row reports the total row count.

Usage

av_overview_summary(obj, extra_cols = NULL, balance_by = NULL)

Arguments

obj

An object of class AlphaVarSet.

extra_cols

Character vector of additional column names (internal names as they exist in obj$data) to include in the summary.

balance_by

Character or NULL. Variable to balance the score statistics over (e.g. "output_type"). When NULL (default), mean_score and median_score are computed over all rows, which weights each modality by its track count (CHIP_HISTONE contributes far more rows than CAGE). When set, a two-step aggregation (within each element, then across elements) gives every element equal weight. Must differ from the active score column.

Value

An object of class AlphaVarOverview, a named list with:

$summary

Tibble with columns field, n_unique, n_missing, n_empty.

$score_col

Name of the currently active score column.

$mean_score

Mean of the active score column (balanced if balance_by is set).

$median_score

Median of the active score column (balanced if balance_by is set).

$balance_by

The balancing variable, or NULL when the statistics are unbalanced.

$breakdowns

Named list, initially empty. Populate with av_overview_breakdown() results for reuse in reports or Shiny.

Details

The default tracked fields are variant_id, coords, gene, modality, transcription_factor, histone_mark, and biosample_name. Fields not present in the data are silently skipped. Fields in extra_cols that are not found in the data produce a warning and are skipped.

Examples

example_file <- system.file("extdata", "bcl11a_rs1427407_example.csv", package = "AlphaVaR")
obj <- av_import_csv(example_file)
#> Reading bcl11a_rs1427407_example.csv ...
av_overview_summary(obj)
#> === AlphaVarOverview Summary ===
#> Score: quantile_score | mean: 0.3797  median: 0.4218  (unbalanced)
#> 
#> # A tibble: 8 × 7
#>   field              n_unique pct_unique n_missing pct_missing n_empty pct_empty
#>   <chr>                 <int>      <dbl>     <int>       <dbl>   <int>     <dbl>
#> 1 entries                2676     100            0        0          0         0
#> 2 variant_id                2       0.07         0        0          0         0
#> 3 scored_interval           1       0.04         0        0          0         0
#> 4 gene_name                23       0.86      1712       64.0        0         0
#> 5 output_type              11       0.41         0        0          0         0
#> 6 transcription_fac…      205       7.66      2348       87.7        0         0
#> 7 histone_mark             22       0.82      2356       88.0        0         0
#> 8 biosample_name          620      23.2          4        0.15       0         0
av_overview_summary(obj, extra_cols = c("biosample_type", "data_source"))
#> === AlphaVarOverview Summary ===
#> Score: quantile_score | mean: 0.3797  median: 0.4218  (unbalanced)
#> 
#> # A tibble: 10 × 7
#>    field             n_unique pct_unique n_missing pct_missing n_empty pct_empty
#>    <chr>                <int>      <dbl>     <int>       <dbl>   <int>     <dbl>
#>  1 entries               2676     100            0        0          0         0
#>  2 variant_id               2       0.07         0        0          0         0
#>  3 scored_interval          1       0.04         0        0          0         0
#>  4 gene_name               23       0.86      1712       64.0        0         0
#>  5 output_type             11       0.41         0        0          0         0
#>  6 transcription_fa…      205       7.66      2348       87.7        0         0
#>  7 histone_mark            22       0.82      2356       88.0        0         0
#>  8 biosample_name         620      23.2          4        0.15       0         0
#>  9 biosample_type           5       0.19         4        0.15       0         0
#> 10 data_source              4       0.15         4        0.15       0         0
av_overview_summary(obj, balance_by = "output_type")
#> === AlphaVarOverview Summary ===
#> Score: quantile_score | mean: 0.3869  median: 0.4358  (balanced by output_type)
#> 
#> # A tibble: 8 × 7
#>   field              n_unique pct_unique n_missing pct_missing n_empty pct_empty
#>   <chr>                 <int>      <dbl>     <int>       <dbl>   <int>     <dbl>
#> 1 entries                2676     100            0        0          0         0
#> 2 variant_id                2       0.07         0        0          0         0
#> 3 scored_interval           1       0.04         0        0          0         0
#> 4 gene_name                23       0.86      1712       64.0        0         0
#> 5 output_type              11       0.41         0        0          0         0
#> 6 transcription_fac…      205       7.66      2348       87.7        0         0
#> 7 histone_mark             22       0.82      2356       88.0        0         0
#> 8 biosample_name          620      23.2          4        0.15       0         0