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Build a library-preparation QC report card

Source: R/qc_report_card.R
library_preparation_report_card.Rd

library_preparation_report_card() evaluates Porkchop-derived library-preparation evidence against pass/warn/fail checks for reporting and review. It consumes R-native evidence tables returned by library_kit_candidates(), library_adapter_primer_evidence(), library_barcode_evidence(), and library_cdna_primer_evidence(); it does not call Porkchop directly.

Usage

library_preparation_report_card(
  kit_candidates = NULL,
  adapter_primer = NULL,
  barcode = NULL,
  cdna = NULL,
  expected_kit_id = NULL,
  thresholds = library_preparation_report_card_thresholds(),
  schema_version = "flounder.library_preparation_report_card.v1"
)

Arguments

kit_candidates

Optional library_kit_candidates() data frame.

adapter_primer

Optional library_adapter_primer_evidence() data frame.

barcode

Optional library_barcode_evidence() data frame.

cdna

Optional library_cdna_primer_evidence() data frame.

expected_kit_id

Optional scalar expected kit id from run metadata or a user-supplied review context.

thresholds

Named threshold list. Defaults to library_preparation_report_card_thresholds().

schema_version

Schema version label to attach to the returned table.

Value

A tibble using the standard report-card schema: schema_version, check_id, check_label, status, observed_value, warn_threshold, fail_threshold, comparator, and details.

Examples

kit_candidates <- data.frame(
  kit_id = "SQK-LSK114",
  normalized_score = 0.9,
  support_level = "supported",
  lifecycle_status = "current"
)
library_preparation_report_card(
  kit_candidates = kit_candidates,
  expected_kit_id = "SQK-LSK114"
)
#> # A tibble: 5 × 9
#>   schema_version       check_id check_label status observed_value warn_threshold
#>   <chr>                <chr>    <chr>       <chr>           <dbl>          <dbl>
#> 1 flounder.library_pr… library… Unexpected… pass                0           0   
#> 2 flounder.library_pr… library… Adapter mo… warn               NA           0.2 
#> 3 flounder.library_pr… library… Barcode am… warn               NA           0.05
#> 4 flounder.library_pr… library… cDNA parti… warn               NA           0.2 
#> 5 flounder.library_pr… library… Unsupporte… pass                0           0   
#> # ℹ 3 more variables: fail_threshold <dbl>, comparator <chr>, details <chr>