https://github.com/ramiromagno/karlen

Real-Time PCR Data Sets by Karlen et al. (2007)
https://github.com/ramiromagno/karlen

qpcr r

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Real-Time PCR Data Sets by Karlen et al. (2007)

• Host: GitHub
• URL: https://github.com/ramiromagno/karlen
• Owner: ramiromagno
• License: cc-by-4.0
• Created: 2024-04-26T15:24:11.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2024-04-28T14:25:14.000Z (8 months ago)
• Last Synced: 2024-11-27T22:42:06.846Z (about 1 month ago)
• Topics: qpcr, r
• Language: R
• Homepage: https://rmagno.eu/karlen/
• Size: 5.81 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE.md

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# karlen

[![CRAN status](https://www.r-pkg.org/badges/version/karlen)](https://CRAN.R-project.org/package=karlen)

[![R-CMD-check](https://github.com/ramiromagno/karlen/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ramiromagno/karlen/actions/workflows/R-CMD-check.yaml)

`{karlen}` provides real-time PCR data sets by Karlen et al. (2007) in tidy

format.

## Installation

``` r

install.packages("karlen")

```

## Data

The raw PCR amplification curve data by Karlen et al. (2007) is provided as one

single eponymously named data set: `karlen`. In the original publication each

data set pertaining one PCR plate is provided as a separate spreadsheet file.

The column `plate` in `karlen` distinguishes each data set.

The `karlen` data set comprises quantitative real-time PCRs for

four samples (S1 thru S4), for seven amplicons targeting seven genes: Cav1,

Ctfg, Eln, Fn1, Rpl27, Hspg2, Serpine1.

For each sample/target combination a dilution series was performed. One PCR

plate was used per amplicon, except for Rpl27 (L27) that was assayed twice

(plates L27_1 and L27_2). The `target` column indicates the mouse gene symbol

matching the targeted amplicon.

```{r}

library(ggplot2)

library(dplyr, warn.conflicts = FALSE)

library(karlen)

karlen |>

  dplyr::distinct(plate, target, sample, sample_type) |>

  print(n = Inf)

```

Two dilution series schemes were assayed:

1. Scheme 1 (Cav1, Eln, Hspg2, Serpine1): 1-fold, 10-fold, 50-fold, and 100-fold;

2. Scheme 2 (Ctgf, Rpl27, Fn1): 1-fold, 10-fold, 50-fold, 100-fold and 1000-fold (two replicates only).

```{r}

karlen |>

  dplyr::filter(sample_type == "std") |>

  dplyr::distinct(plate, target, dilution) |>

  print(n = Inf)

```

Visualization of amplification curves (NTC curves are omitted):

```{r example, dev='png', dpi=400, fig.width=10, fig.height=15}

karlen |>

  dplyr::filter(sample_type != "ntc") |>

  ggplot(aes(x = cycle, y = fluor, group = well, col = as.factor(dilution))) +

  geom_line(linewidth = 0.1) +

  geom_point(size = 0.05) +

  facet_grid(rows = vars(plate), cols = vars(sample), scales = "free_y") +

  labs(color = "Fold dilution")

```

## References

Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza, and Nicolas

Mermod. _Statistical significance of quantitative PCR_. BMC Bioinformatics 8, 131

(2007). doi: [10.1186/1471-2105-8-131](https://doi.org/10.1186/1471-2105-8-131).