Plan PCR experiment

Usage

pcr_plan(
  data,
  n_primers,
  format = 384,
  exclude_border = TRUE,
  primer_names = NULL,
  headless = TRUE,
  has_names = TRUE
)

Arguments

data: a data.frame, with samples as the first column (if has_names = TRUE) and RNA concentrations as the second (or first, if has_names = FALSE)
n_primers: integer. Number of primers to be used in the experiment.
format: integer. 96 or 384 - the number of wells of the plate planned to be used
exclude_border: logical. Should the border be excluded to avoid edge effects? Default is TRUE.
primer_names: character vector. Names of primers.
headless: logical. If FALSE, return invisible and redirect to shiny application.
has_names: logical. Is the first column the names of the samples?

Value

a named list

Examples

dummy_rna_conc |>
  pcr_plan(n_primers = 3)
#> $mm_prep
#> # A tibble: 4 x 2
#>   reagent             vol
#>   <chr>             <dbl>
#> 1 2X RT-PCR Buffer  206. 
#> 2 Primer             20.6
#> 3 25X RT-PCR Enzyme  16.5
#> 4 Nuclease Free H2O 103. 
#> 
#> $sample_prep
#> # A tibble: 8 x 7
#>   sample    conc dilution_factor diluted_concentr~ diluted_rna_to_~ water_to_add
#>   <chr>    <dbl>           <int>             <dbl>            <dbl>        <dbl>
#> 1 24hr_DM~ 127.                1             127.              1.18         28.8
#> 2 48hr_DM~  93                 1              93               1.61         28.4
#> 3 24hr_1u~ 143.                1             143.              1.05         29.0
#> 4 48hr_1u~  67.1               1              67.1             2.24         27.8
#> 5 24hr_DM~  88.3               1              88.3             1.70         28.3
#> 6 48hr_DM~ 124.                1             124.              1.21         28.8
#> 7 24hr_1u~  94.2               1              94.2             1.59         28.4
#> 8 48hr_1u~  80.2               1              80.2             1.87         28.1
#> # ... with 1 more variable: final_vol <dbl>
#> 
#> $plate
#> # A tibble: 384 x 10
#> # Groups:   primer [4]
#>    primer sample col   row   lane_v lane_h available_well sample_name
#>    <fct>  <fct>  <fct> <fct>  <int>  <int> <lgl>          <chr>      
#>  1 1      1      2     b          1      1 TRUE           NA         
#>  2 1      1      3     b          1      1 TRUE           24hr_DMSO_1
#>  3 1      1      4     b          1      1 TRUE           NA         
#>  4 1      2      2     c          1      1 TRUE           NA         
#>  5 1      2      3     c          1      1 TRUE           48hr_DMSO_1
#>  6 1      2      4     c          1      1 TRUE           NA         
#>  7 1      3      2     d          1      1 TRUE           NA         
#>  8 1      3      3     d          1      1 TRUE           24hr_1uM_1 
#>  9 1      3      4     d          1      1 TRUE           NA         
#> 10 1      4      2     e          1      1 TRUE           NA         
#> # ... with 374 more rows, and 2 more variables: plotting_name <chr>,
#> #   primer_name <chr>
#> 
#> $n_primers
#> [1] 3
#> 
#> $format
#> [1] "384"
#> 
#> $exclude_border
#> [1] TRUE
#> 
#> $primer_names
#> NULL
#>