software.Rmd

---
title: 2. Software for Proteomics Data Analysis (PDA) 
author: "Lieven Clement"
date: "[statOmics](https://statomics.github.io), Ghent University"
output:
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      theme: flatly      
      code_download: false
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---

<a rel="license" href="https://creativecommons.org/licenses/by-nc-sa/4.0"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a>

- Install [R version 4.1 or higher] (https://cran.r-project.org/)
- Install [Rstudio](https://www.rstudio.com/products/rstudio/download/)
- Install *msqrob2*, start R and run the following command.

```
if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
BiocManager::install("msqrob2")
```

- Participants who want to use the graphical user interface (GUI) can install the msqrob2gui shiny app, start R and run the following commands

```
if(!requireNamespace("BiocManager", quietly = TRUE)) {
 install.packages("BiocManager")
}
if(!requireNamespace("remotes", quietly = TRUE)) {
 BiocManager::install("remotes")
}
BiocManager::install("statomics/msqrob2gui")
```

- check if your installation is working with the following example

``` 
library(msqrob2)
data(pe)
pe <- aggregateFeatures(pe,i="peptide",fcol="Proteins",name="protein")
pe <- msqrob(pe,i="protein",formula=~condition,modelColumnName="rlm")
getCoef(rowData(pe[["protein"]])$rlm[[1]])
```