Create library prep quality control data
pcr_lib_qc.RdCreate library prep quality control data
Value
a named list with:
standards Data for individual standards, including calculated dilutions, given and calculated quantities, raw Ct, etc.
samples Data for individual samples, including calculated concentrations, raw Ct, etc.
sample_summary Summary statistics for samples grouped by replicates
standard_summary Summary statistics for standards groupd by replicates
outliers Data for individual samples and standards with and without their putative outliers (
po) per replicate group
Details
While the output of this function on its own is can theoretically be
used to gauge library quality, it is best used in conjunction with a
function like pcr_lib_calc_report
Examples
system.file("extdata", "untidy-standard-curve.xlsx", package = "amplify") |>
pcr_tidy(pad_zero = TRUE) |>
pcr_lib_calc() |>
pcr_lib_qc()
#> $standards
#> # A tibble: 13 x 19
#> # Groups: sample_name [5]
#> sample_name task quantity_mean concentration quantity quant_actual dil
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 2 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 3 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 4 Standard 02 STANDARD NA NA 0.680 0.734 9.27
#> 5 Standard 02 STANDARD NA NA 0.680 0.734 9.27
#> 6 Standard 03 STANDARD NA NA 0.0680 0.0603 12.2
#> 7 Standard 03 STANDARD NA NA 0.0680 0.0603 12.2
#> 8 Standard 03 STANDARD NA NA 0.0680 0.0603 12.2
#> 9 Standard 04 STANDARD NA NA 0.00680 0.00568 10.6
#> 10 Standard 04 STANDARD NA NA 0.00680 0.00568 10.6
#> 11 Standard 04 STANDARD NA NA 0.00680 0.00568 10.6
#> 12 Standard 05 STANDARD NA NA 0.000680 0.000417 13.6
#> 13 Standard 05 STANDARD NA NA 0.000680 0.000417 13.6
#> # ... with 12 more variables: slope <dbl>, efficiency <dbl>, r2 <dbl>,
#> # ct <dbl>, no_po_mean <dbl>, no_po_sd <dbl>, keep <lgl>, keep_temp <lgl>,
#> # mean_adj <dbl>, sd_adj <dbl>, quant_adj <dbl>, z <dbl>
#>
#> $samples
#> # A tibble: 42 x 19
#> # Groups: sample_name [16]
#> sample_name task quantity_mean concentration quantity quant_actual dil
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Sample 06 UNKNOWN 2.04 2039. 2.06 2.06 NA
#> 2 Sample 06 UNKNOWN 2.04 2039. 2.12 2.12 NA
#> 3 Sample 06 UNKNOWN 2.04 2039. 1.94 1.94 NA
#> 4 Sample 12 UNKNOWN 1.89 1893. 1.93 1.93 NA
#> 5 Sample 12 UNKNOWN 1.89 1893. 1.88 1.88 NA
#> 6 Sample 12 UNKNOWN 1.89 1893. 1.87 1.87 NA
#> 7 Sample 04 UNKNOWN 1.69 1694. 1.62 1.62 NA
#> 8 Sample 04 UNKNOWN 1.69 1694. 1.84 1.84 NA
#> 9 Sample 04 UNKNOWN 1.69 1694. 1.62 1.62 NA
#> 10 Sample 16 UNKNOWN 1.49 1493. 1.46 1.46 NA
#> # ... with 32 more rows, and 12 more variables: slope <dbl>, efficiency <dbl>,
#> # r2 <dbl>, ct <dbl>, no_po_mean <dbl>, no_po_sd <dbl>, keep <lgl>,
#> # keep_temp <lgl>, mean_adj <dbl>, sd_adj <dbl>, quant_adj <dbl>, z <dbl>
#>
#> $sample_summary
#> # A tibble: 16 x 3
#> sample_name quantity_mean quant_adj
#> <chr> <dbl> <dbl>
#> 1 Sample 01 0.599 0.599
#> 2 Sample 02 1.05 1.05
#> 3 Sample 03 1.37 1.39
#> 4 Sample 04 1.69 1.62
#> 5 Sample 05 0.903 0.888
#> 6 Sample 06 2.04 2.09
#> 7 Sample 07 1.13 1.15
#> 8 Sample 08 1.09 1.09
#> 9 Sample 09 1.22 1.22
#> 10 Sample 10 1.07 1.07
#> 11 Sample 11 1.03 1.03
#> 12 Sample 12 1.89 1.87
#> 13 Sample 13 0.583 0.583
#> 14 Sample 14 1.22 1.17
#> 15 Sample 15 0.713 0.713
#> 16 Sample 16 1.49 1.42
#>
#> $standard_summary
#> # A tibble: 5 x 4
#> sample_name dil quantity_mean quant_actual
#> <chr> <dbl> <dbl> <dbl>
#> 1 Standard 01 0 6.80 6.80
#> 2 Standard 02 9.27 0.680 0.734
#> 3 Standard 03 12.2 0.0680 0.0603
#> 4 Standard 04 10.6 0.00680 0.00568
#> 5 Standard 05 13.6 0.000680 0.000417
#>
#> $outliers
#> # A tibble: 58 x 19
#> # Groups: sample_name [22]
#> sample_name task quantity_mean concentration quantity quant_actual dil
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 NA NTC NA NA NA NA NA
#> 2 NA NTC NA NA NA NA NA
#> 3 NA NTC NA NA NA NA NA
#> 4 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 5 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 6 Standard 01 STANDARD NA NA 6.80 6.80 0
#> 7 Standard 02 STANDARD NA NA 0.680 0.734 9.27
#> 8 Standard 02 STANDARD NA NA 0.680 0.734 9.27
#> 9 Standard 03 STANDARD NA NA 0.0680 0.0603 12.2
#> 10 Standard 03 STANDARD NA NA 0.0680 0.0603 12.2
#> # ... with 48 more rows, and 12 more variables: slope <dbl>, efficiency <dbl>,
#> # r2 <dbl>, ct <dbl>, no_po_mean <dbl>, no_po_sd <dbl>, keep <lgl>,
#> # keep_temp <lgl>, mean_adj <dbl>, sd_adj <dbl>, quant_adj <dbl>, z <dbl>
#>