Summarise key QC fields per sample

Return a tidy summary of the most relevant QC fields from a qseaSet sampleTable. If core library metrics are missing, they are first added via addLibraryInformation().

getSampleQCSummary(qseaSet)

Arguments

qseaSet

qseaSet. Input object from which to extract QC fields. Default: none (must be supplied).

Value

A tibble with one row per sample containing:

• sample_name

• any available QC columns matching valid_fragment, relH, hyperStable, or ichorTumo. Columns not present in the sampleTable are silently omitted.

Details

If the sampleTable lacks library metrics (e.g., valid_fragments), the function calls addLibraryInformation() to populate them. The output keeps sample_name and any columns whose names match the regex "valid_fragment|relH|hyperStable|ichorTumo" (if present), then orders rows by sample_name.

See also

qsea::getSampleTable(), addLibraryInformation(), addHyperStableFraction()

Examples

data("exampleTumourNormal", package = "mesa")

# QC summary (adds library info if missing), ordered by sample_name
exampleTumourNormal %>%
    getSampleQCSummary() %>%
    head()
#> # A tibble: 6 × 5
#>   sample_name valid_fragments  relH input_valid_fragments input_relH
#>   <chr>                 <int> <dbl>                 <int>      <dbl>
#> 1 Colon1_N            3745354  5.57               2011862       1.51
#> 2 Colon1_T            7428804  4.92               3443167       1.45
#> 3 Colon2_N            4195483  5.40               1767031       1.61
#> 4 Colon2_T            5878535  5.69               3146633       1.47
#> 5 Lung1_N             7747154  4.46               2667740       1.44
#> 6 Lung1_T             5208468  4.41               1964050       1.48