batsch

Real-Time PCR Data Sets by Batsch et al. (2008)

https://github.com/ramiromagno/batsch

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Real-Time PCR Data Sets by Batsch et al. (2008)

README.Rmd

---
output: github_document
---



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

# batsch


[![CRAN status](https://www.r-pkg.org/badges/version/batsch)](https://CRAN.R-project.org/package=batsch)
[![R-CMD-check](https://github.com/ramiromagno/batsch/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/batsch/actions/workflows/R-CMD-check.yaml)


`{batsch}` provides real-time PCR data sets by Batsch et al. (2008) in tidy
format. There are five data sets bundled with this package, one for each PCR
target:

- `SLC6A14r` for *rat SLC6A14*
- `SLC22A13h` for *human SLC22A13*
- `EMTp` for *pig EMT*
- `ETTch` for *chicken ETT*
- `GAPDHh` for *human GAPDH*

Each data set comprises a five-point, four-fold dilution series. For each
concentration there are three replicates. Each amplification curve is 45 cycles
long.

## Installation

Install `{batsch}` from CRAN:

``` r
# Install from CRAN
install.packages("batsch")
```

You can instead install the development version of `{batsch}` from GitHub:

``` r
# install.packages("remotes")
remotes::install_github("ramiromagno/batsch")
```

## Usage

### Rat SLC6A14

```{r dpi=300, fig.width=8, fig.height=4}
library(batsch)

SLC6A14r |>
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(dilution, replicate),
    col = as.factor(dilution)
  )) +
  geom_line(linewidth = 0.5) +
  labs(y = "Raw fluorescence", colour = "Dilution factor", title = "Rat SLC6A14") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

### Human SLC22A13

```{r dpi=300, fig.width=8, fig.height=4}
SLC22A13h |>
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(dilution, replicate),
    col = as.factor(dilution)
  )) +
  geom_line(linewidth = 0.5) +
  labs(y = "Raw fluorescence", colour = "Dilution factor", title = "Human SLC22A13") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

### Pig EMT

```{r dpi=300, fig.width=8, fig.height=4}
EMTp |>
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(dilution, replicate),
    col = as.factor(dilution)
  )) +
  geom_line(linewidth = 0.5) +
  labs(y = "Raw fluorescence", colour = "Dilution factor", title = "Pig EMT") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

### Chicken ETT

```{r dpi=300, fig.width=8, fig.height=4}
ETTch |>
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(dilution, replicate),
    col = as.factor(dilution)
  )) +
  geom_line(linewidth = 0.5) +
  labs(y = "Raw fluorescence", colour = "Dilution factor", title = "Chicken ETT") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

### Human GAPDH

```{r dpi=300, fig.width=8, fig.height=4}
GAPDHh |>
  ggplot(mapping = aes(
    x = cycle,
    y = fluor,
    group = interaction(dilution, replicate),
    col = as.factor(dilution)
  )) +
  geom_line(linewidth = 0.5) +
  labs(y = "Raw fluorescence", colour = "Dilution factor", title = "Human GAPDH") +
  guides(color = guide_legend(override.aes = list(size = 0.5)))
```

## Code of Conduct
  
Please note that the `{batsch}` project is released with a [Contributor Code of
Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By
contributing to this project, you agree to abide by its terms.

## References

- Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig & Dirk Gründemann. _Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence_. BMC Bioinformatics 9:95 (2008). doi: [10.1186/1471-2105-9-95](https://doi.org/10.1186/1471-2105-9-95).

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