(Re)calculate rq for a given sample
pcr_rq.Rd(Re)calculate rq for a given sample
Arguments
- data
A dataset output from pcr_tidy/pcr_control
- relative_sample
A sample to set others relative to (eg my_dmso_sample)
Examples
dat_path <- system.file("extdata", "untidy-pcr-example.xls", package = "amplify")
pcr_tidy(dat_path) |>
pcr_rq("U6D1")
#> # A tibble: 267 x 39
#> # Groups: target_name [5]
#> omit sample_name target_name task reporter quencher quantity quantity_mean
#> <lgl> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 2 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 3 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 4 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 5 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 6 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 7 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 8 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 9 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 10 FALSE RD1 GENE4 UNKNO~ FAM NFQ-MGB NA NA
#> # ... with 257 more rows, and 31 more variables: quantity_sd <dbl>, rq <dbl>,
#> # rq_min <dbl>, rq_max <dbl>, ct_mean <dbl>, ct_sd <dbl>, delta_ct <dbl>,
#> # delta_ct_mean <dbl>, delta_ct_se <dbl>, delta_delta_ct <dbl>,
#> # automatic_ct_threshold <lgl>, ct_threshold <dbl>, automatic_baseline <lgl>,
#> # comments <chr>, analysis_type <chr>, control <chr>, conf_int <chr>,
#> # ref_samp <chr>, plate_type <chr>, exp_type <chr>, rep <int>, ct <dbl>,
#> # well <chr>, well_row <dbl>, well_col <dbl>, well_position <chr>, ...
# Can also be run after using pcr_control:
pcr_tidy(dat_path) |>
pcr_control("GAPDH") |>
pcr_rq("U6D1")
#> # A tibble: 267 x 39
#> # Groups: target_name [5]
#> omit sample_name target_name task reporter quencher quantity quantity_mean
#> <lgl> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 2 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 3 FALSE RD1 GENE1 UNKNO~ FAM NFQ-MGB NA NA
#> 4 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 5 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 6 FALSE RD1 GENE2 UNKNO~ FAM NFQ-MGB NA NA
#> 7 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 8 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 9 FALSE RD1 GENE3 UNKNO~ FAM NFQ-MGB NA NA
#> 10 FALSE RD1 GENE4 UNKNO~ FAM NFQ-MGB NA NA
#> # ... with 257 more rows, and 31 more variables: quantity_sd <dbl>, rq <dbl>,
#> # rq_min <dbl>, rq_max <dbl>, ct_mean <dbl>, ct_sd <dbl>, delta_ct <dbl>,
#> # delta_ct_mean <dbl>, delta_ct_se <dbl>, delta_delta_ct <dbl>,
#> # automatic_ct_threshold <lgl>, ct_threshold <dbl>, automatic_baseline <lgl>,
#> # comments <chr>, analysis_type <chr>, control <chr>, conf_int <chr>,
#> # ref_samp <chr>, plate_type <chr>, exp_type <chr>, rep <int>,
#> # delta_ct_sd <dbl>, df <dbl>, t <dbl>, ct <dbl>, well <chr>, ...