README.Rmd

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output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# qp <a href="https://kaiaragaki.github.io/qp/"><img src="man/figures/logo.png" align="right" height="138" alt="qp website" /></a>

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`qp` serves as a robust toolkit for working with MicroBCA assays. Currently, the protocol it's best served for is [here](https://kai.quarto.pub/bok/western-blot.html#protein-quantification).

## Installation

You can install the development version of qp from [GitHub](https://github.com/) with:

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

## Quickstart

If you have a nicely formatted plate with no surprises (that is, it follows [this](https://kai.quarto.pub/bok/western-blot.html#protein-quantification) protocol), you should really only need to plug it in to `qp` and let it rip:

```{r}
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
)
```

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

```{r}
summary <- qp_summarize(out)

qp_dilute(summary, target_vol = 15, remove_standards = TRUE)
```

Or make a plot to assess quality:

```{r, fig.width=10, out.width="100%"}
qp_plot_standards(out)
```