README.Rmd

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# syntR <img src="https://raw.githubusercontent.com/ksamuk/syntR/master/inst/figures/logo.png" align="right" width="120" height="135" />

syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers. 

### Documentation
[The documentation and tutorial for syntR can be found here](https://ksamuk.github.io/syntR/index.html)

### Installation

You can install syntR from Github with:

```{r, eval = FALSE}
install.packages("devtools")
devtools::install_github("ksamuk/syntR")
```

### Example

Find synteny blocks shared between *Helianthus petiolaris* and *Helianthus annus* (provided as example data):

```{r, eval = FALSE}
# load the syntR library
library("syntR")

# load data
data(ann_pet_map)

# convert data to a single ordered scale
map_list <- make_one_map(ann_pet_map)

# find synteny blocks
synt_blocks <- find_synteny_blocks(map_list, max_clust_range = 2, max_nn_dist = 10, plots = TRUE)

# print the resulting synteny blocks dataframe
synt_blocks[[2]]
```

### Authors

[Katherine Ostevik](http://www.kateostevik.com/) and [Kieran Samuk](https://ksamuk.github.io/).

### See Also

[GRIMM](http://grimm.ucsd.edu/GRIMM/) - A tool for analyzing rearrangements in pairs of genomes, including unichromosomal and multichromosomal genomes, and signed and unsigned data. 

[Flagel et al. 2018](https://www.biorxiv.org/content/early/2018/05/26/330159) - An example of a more formal model-based approach to a similar problem.