Skip to contents

balselr

What is balselr?

Balancing selection with R allows you to run NCD statistics to detect long-term balancing selection in genomic datasets as described in the paper: Bitarello et al. (2018)

How to cite us

For now, please cite us as follows:

Hansell, D and Bitarello, B (2026). balselr: Balancing Selection in R Zenodo. https://doi.org/10.5281/zenodo.18148850

Thank you!

Installation

You can install the development version of balselr from GitHub with:

# install.packages("devtools")
library(devtools)
devtools::install_github("bitarellolab/balselr")
library(balselr)

Example

This is a basic example which shows you how to read in a vcf file:

read_vcf(x = system.file(package = "balselr", "example.vcf"))

This is an example which shows how to parse a vcf file and output an input file for ncd1:

parse_vcf(
        infile = system.file(package = "balselr", "example.vcf"),
        n0 = 108,
        type = "ncd1"
)

This is an example which shows how to parse a vcf file and output an input file for ncd2:

parse_vcf(
        infile = system.file(package = "balselr", "example.vcf"),
        n0 = 108,
        n1 = 2,
        type = "ncd2"
)

Run ncd1 (tf=0.5) with a 3000 basepair window and a minimum of 8 informative sites per window using 2 cores:

data(ncd1_input)
ncd1(x = ncd1_input, tf = 0.5, w = 3000, ncores = 2, minIS=8)

Run ncd2 (tf=0.5) with a 3000 basepair window and a minimum of 2 informative sites per window using 2 cores:

data(ncd2_input)
ncd2(x = ncd2_input, tf = 0.5, w = 3000, ncores = 2, minIS=2)