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Build a run-level QC report card

Source: R/qc_report_card.R
qc_report_card.Rd

qc_report_card() evaluates a run summary against pass/warn/fail threshold checks. It is intentionally limited to sequencing-summary-derived evidence until POD5, BAM/Bamana, and Porkchop contracts are available.

Usage

qc_report_card_thresholds()

qc_report_card(
  x,
  thresholds = qc_report_card_thresholds(),
  barcode_composition = NULL,
  schema_version = "flounder.qc_report_card.v1"
)

Arguments

x

A SequencingSummary object, a sequencing-summary file path, a normalised sequencing-summary data frame/tibble, or a qc_run_summary() one-row tibble.

thresholds

Named threshold list. Defaults to qc_report_card_thresholds().

barcode_composition

Optional qc_barcode_composition() tibble. When omitted and x is sequencing-summary-like, it is derived automatically.

schema_version

Schema version label to attach to the returned table.

Value

qc_report_card_thresholds() returns a named list of warn/fail thresholds.

qc_report_card() returns a tibble with one row per report-card check:

schema_version

Report-card schema identifier.

check_id

Stable lower-snake-case check identifier.

check_label

Human-readable check label.

status

One of pass, warn, or fail.

observed_value

Numeric value evaluated by the check.

warn_threshold

Warning threshold used by the check.

fail_threshold

Failure threshold used by the check.

comparator

Threshold direction: minimum or maximum.

details

Short explanatory text for report rendering.

Details

Default thresholds are:

pass_fraction_min

warn < 0.85, fail < 0.70

mean_qscore_min

warn < 10, fail < 8

n50_read_length_min

warn < 1000 bases, fail < 500 bases

total_bases_min

warn < 1,000,000 bases, fail < 100,000 bases

channel_count_min

warn < 64 channels, fail < 16 channels

unclassified_fraction_max

warn > 0.10, fail > 0.25

barcode_max_fraction

warn > 0.60, fail > 0.80

Missing observed values are reported as warn with explanatory detail text so report consumers can distinguish absent evidence from explicit failure.

Examples

summary_file <- flnDr("sequencing_summary.txt.bz2")
qc_report_card(summary_file)
#> # A tibble: 7 × 9
#>   schema_version       check_id check_label status observed_value warn_threshold
#>   <chr>                <chr>    <chr>       <chr>           <dbl>          <dbl>
#> 1 flounder.qc_report_… pass_fr… Pass read … warn            0.836           0.85
#> 2 flounder.qc_report_… mean_qs… Mean read … warn            9.48           10   
#> 3 flounder.qc_report_… n50_rea… Read lengt… pass        26855            1000   
#> 4 flounder.qc_report_… total_b… Total base… pass    147095512         1000000   
#> 5 flounder.qc_report_… channel… Active cha… pass          502              64   
#> 6 flounder.qc_report_… unclass… Unclassifi… pass            0               0.1 
#> 7 flounder.qc_report_… barcode… Largest ba… warn           NA               0.6 
#> # ℹ 3 more variables: fail_threshold <dbl>, comparator <chr>, details <chr>