README.Rmd

---
output: github_document
---

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

# analyzeGC

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This package was built for educational and research purposes in the field of chemical ecology. 
The objective was to provide a tool set for using R to analyze GC, and in particular GC-MS (GC coupled with Mass-spectrometry) data, to establish a standardized and reproducible workflow.
As I mainly work with cuticular hydrocarbons (CHCs) the workflow implied within the package was designed considering that specific type of data. 
However, the workflow it suggests and most of the functions can be used for analyzing other types of chemical ecology GC data.

The package relies on the [GCalignR](https://github.com/mottensmann/GCalignR) package for the alignment of GC peaks data across samples, based on the  retention time of the peaks.
A wrapper around the `GCalignR::align_chromatograms` is defined within the package for this purpose.

The rest of the functions of the package are oriented to aid the further correction of the peaks alignment, and preparation of the data for its statistical analysis within R.

## Installation

You can install the development version of analyzeGC from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("dsrodriguezl/analyzeGC"
  , dependencies = TRUE
  , build_vignettes = TRUE)
```

## Get started

To get started read the vignettes:

```r
browseVignettes("analyzeGC")
```