README.Rmd

---
title: "Expression of elongase- and desaturase-encoding genes shapes the cuticular hydrocarbon profiles of honey bees"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

This repository contains all the data and code needed to reproduce the analyses of the study titled "Expression of elongase- and desaturase-encoding genes shapes the cuticular hydrocarbon profiles of honey bees".

The repository corresponds to an R project repository that can be directly open in RStudio via the des&elo-gene-exp-shapes-honey-bee-CHCs.Rproj file.
This makes the R project portable, as the working directory is automatically set within RStudio to the folder of the repository.

This R project uses the package renv to create a reproducible environment.
To download and install all project's dependencies, use `renv::restore()` the first time you open the R project in RStudio.
This will ensure you can run the code properly to reproduce the analyses of the study.
See <https://rstudio.github.io/renv/> for more details on the usage of renv package.

## Data:

All data related to the study is stored in the "data" folder.
The folder is divided in three following subfolders:

-   **raw:** Contains data files (i.e. CSV files) with the data as originally obtained.
    -   raw/samples_list.csv contains the samples metadata.
    -   raw/gcms-integration folder contains CSV files with GC-MS integration results of every sample. It is divided into two sub-folders, corresponding to the two batches in which the samples were run in the GC-MS machine(s).
    -   raw/qPCR folder contains CSV files with measured Ct values for each qPCR run. Files in sub-folder "samples_runs" correspond to the measured Ct values for the analyzed samples, the six CSV files outside of this sub-folder correspond to the standard curves.
-   **tmp:** Temporary data files produced during the processing of the raw data, in order to prepare the data set(s) for statistical analysis.
-   **processed:** Final data files (i.e. Rdata files) with the final data set(s), ready for statistical analyses.

## Code:

Analysis.R is the master script.
It contains the code to replicate the entire set of analyses of the study.
It also generates the figures for the manuscript, storing them in the folder "figs".
The code in the script relies on the des&elo-gene-exp-shapes-honey-bee-CHCs.Rproj to determine the working directory within RStudio.

The folder "scripts" contain R scripts with code that is needed for the Analysis.R script to perform the analyses of the study.