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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%"
)
```
# vermeulen
<!-- badges: start -->
[](https://CRAN.R-project.org/package=vermeulen)
[](https://github.com/ramiromagno/vermeulen/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
`{vermeulen}` provides the Biomarker data set by [Vermeulen et al.
(2009)](https://doi.org/10.1016/S1470-2045(09)70154-8) in tidy format.
This data set is for a real-time quantitative PCR experiment that comprises:
- The raw fluorescence data of 24,576 amplification curves.
- 64 targets: 59 genes of interest and 5 reference genes.
- 366 neuroblastoma cDNA samples and 18 dilution series samples.
## Installation
Install `{vermeulen}` from CRAN:
``` r
# Install from CRAN
install.packages("vermeulen")
```
You can instead install the development version of `{vermeulen}` from GitHub:
``` r
# install.packages("remotes")
remotes::install_github("ramiromagno/vermeulen")
```
## Usage
Because of CRAN size limits the data is not provided at installation time. The
data can be retrieved from this GitHub repository after installation with the
function `get_biomarker_dataset()`.
```{r message=FALSE, warning=FALSE}
library(vermeulen)
library(tibble)
library(dplyr)
# Takes a few seconds (downloading from GitHub...)
biomarker <- as_tibble(get_biomarker_dataset())
biomarker
```
Types of samples:
```{r}
count(
distinct(biomarker, plate, well, sample_type, copies, dilution),
sample_type,
copies,
dilution
)
```
## Code of Conduct
Please note that the `{vermeulen}` 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
1. Vermeulen et al.. *Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study*. The Lancet Oncology 10, 663--671 (2009). doi: [10.1016/S1470-2045(09)70154-8](https://doi.org/10.1016/S1470-2045(09)70154-8).
2. Ruijter et al.. *Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications*. Methods 59 32--46 (2013). doi: [10.1016/j.ymeth.2012.08.011](https://doi.org/10.1016/j.ymeth.2012.08.011).