README.Rmd

---
output: github_document
---


```{r, echo = FALSE}
description <- readLines("DESCRIPTION")
rvers <- stringr::str_match(grep("R \\(", description, value = TRUE), "[0-9]{1,4}\\.[0-9]{1,4}\\.[0-9]{1,4}")[1,1]
version <- gsub(" ", "", gsub("Version:", "", grep("Version:", description, value = TRUE)))
```

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```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```
# radiator: an R package for RADseq Data Exploration, Manipulation and Visualization

Most genomic analysis look for patterns and trends with various statistics. 
Bias, noise and outliers can have bounded influence on estimators and interfere
with polymorphism discovery. Avoid bad data exploration and control the impact
of filters on your downstream genetic analysis. Use radiator to: import, explore,
manipulate, visualize, filter, impute and export your GBS/RADseq data.

**radiator** is designed and optimized for fast computations of diploid data 
using Genomic Data Structure [GDS](https://github.com/zhengxwen/gdsfmt) file 
format and data science packages in 
[tidyverse](https://www.tidyverse.org). **radiator** handles VCF files with millions of
SNPs and files of several GB.

## Installation
To try out the dev version of **radiator**, copy/paste the code below:

```{r eval = FALSE}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("thierrygosselin/radiator")
library(radiator)
```

**Note** 

Some Windows OS and Linux OS recently experienced some problems during installations,
linked to CRAN & Bioconductor tango problems:

- If you're experiencing problems with radiator installation see 
[troubleshooting section](https://thierrygosselin.github.io/radiator/articles/rad_genomics_computer_setup.html)
and try the lines below.

- Verify that installing **radiator** also installed the 
[Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/SeqArray.html) 
packages: `gdsfmt` and 
[SeqArray](https://github.com/zhengxwen/SeqArray) with version >= 1.28.1.

```{r eval = FALSE}
devtools::package_info(pkgs = "SeqArray") # to verify version

# If manually installing SeqArray is necessary
install.packages("BiocManager")
BiocManager::install("SeqArray")
```


Web site with additional info: [https://thierrygosselin.github.io/radiator/](https://thierrygosselin.github.io/radiator/)

* [Computer setup and troubleshooting](https://thierrygosselin.github.io/radiator/articles/rad_genomics_computer_setup.html)
* [Learning radiator](https://thierrygosselin.github.io/radiator/articles/get_started.html) and [Overview of features](https://thierrygosselin.github.io/radiator/articles/get_started.html#overview)
* [Vignettes](https://thierrygosselin.github.io/radiator/articles/index.html)

## [Life cycle](https://thierrygosselin.github.io/radiator/articles/life_cycle.html)

radiator is maturing, but in order to make the package better, changes are 
inevitable. Experimental functions will change, argument names will change.
Your codes and workflows might break from time to time until radiator is stable. 
Consequently, depending on your tolerance to change, radiator might not be for you.
Avoid using radiator if you suffer from the Semmelweis reflex. 
Philosophy, major changes and deprecated functions/arguments are documented in
life cycle section of functions. 

* The latest changes are documented ([here](https://thierrygosselin.github.io/radiator/articles/life_cycle.html)) and
in [changelog, versions, new features and bug history](https://thierrygosselin.github.io/radiator/news/index.html)
* Question(s) or problem(s) with radiator, open an [issue](https://github.com/thierrygosselin/radiator/issues/new/choose)
* [Contributions are welcomed](https://github.com/thierrygosselin/radiator/issues/new/choose)