qp

qp serves as a robust toolkit for working with MicroBCA assays. Currently, the protocol it’s best served for is here.

Installation

You can install the development version of qp from GitHub with:

# install.packages("devtools")
devtools::install_github("KaiAragaki/qp")

Quickstart

If you have a nicely formatted plate with no surprises (that is, it follows this protocol), you should really only need to plug it in to qp and let it rip:

library(qp)
f <- system.file("extdata", "absorbances.txt", package = "qp")

# Most of these arguments are defaults
# I'm only writing them out so you can see what options you can set
out <- qp(
  f,
  replicate_orientation = "h",
  sample_names = c("here", "are", "my", "sample", "names"),
  remove_empty = TRUE,
  ignore_outliers = "all",
  standard_scale = c(0, 2^((2:7) - 5)),
  n_replicates = 3,
  wavelength = 562
)
#> Please wait. This will take ~10 seconds.

From this, you can do things like add dilution calculations:

summary <- qp_summarize(out)

qp_dilute(summary, target_vol = 15, remove_standards = TRUE)
#> `target_conc` is missing, using lowest sample concentration
#> # A tibble: 5 × 5
#>   .sample_name sample_type .mean_pred_conc sample_to_add add_to
#>   <chr>        <fct>                 <dbl>         <dbl>  <dbl>
#> 1 here         unknown               1.71           3.97  11.0 
#> 2 are          unknown               1.39           4.85  10.1 
#> 3 my           unknown               0.989          6.85   8.15
#> 4 sample       unknown               1.30           5.23   9.77
#> 5 names        unknown               0.451         15      0

Or make a plot to assess quality:

qp_plot_standards(out)