What is balselr?

Balancing selection with R allows you to run NCD statistics to detect long-term balancing selection in genomic datasets.

Original paper describing the NCD statistics: Bitarello, De Filippo, Teixeira, Schmidt, Kleinert, Meyer & Andrés (2018). Signatures of long-term balancing selection in human genomes. Genome biology and evolution, 10(3), 939-955. Link

Citing

If you have used nitro in a publication and have found it useful, please consider citing it as follows:

Hansell, D. & Bitarello, B. (2024). balselr: balancing selection tests in R. GitHub repository: https://github.com/bitarellolab/balselr.

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)