export_genind_genclone.Rmd

---
title: "Export to genind and genclone"
---


The R packages **adegenet** and **poppr** are popular tools for population genetic analysis.
Here we describe how to convert a vcfR object to a genind and genclone object.


## Data import

We will use the example dataset provided by vcfR.


```{r}
library(vcfR)
data(vcfR_example)
```


## Creating genind objects

The packages **adegenet** and **poppr** use objects of class **genind**.
We can create genind objects with the function **vcfR2genind()**.


```{r genind, eval=TRUE}
my_genind <- vcfR2genind(vcf)
class(my_genind)
my_genind
```


The function `vcfR2genind()` calls `extract.gt()` to create a matrix of genotypes.
This matrix is converted into a genind object with the adegenet function `df2genind()`.


Currently, this function does not scale well to large quantities of data.
This appears to be due  a call to the function adegenet::df2genind (this function was produced prior to high throughput sequencing).
The genlight object is designed to perform better for larger datasets.


## Creating genclone objects


The package **poppr** uses objects of class genclone as well as genind.
Once a genind object has been created, it is fairly straight forward to create a genclone object.


```{r genclone, eval=TRUE}
my_genclone <- poppr::as.genclone(my_genind)
class(my_genclone)
my_genclone
```