r Rpackage("scoreInvHap") genotypes inversions using SNP data. This method computes a similarity score between the available SNPs of an individual and experimental references for the three inversion-genotypes; NN: non-inverted homozygous, NI: inverted heterozygous and II: inverted homozygous. Individuals are classified into the inversion-genotypes with the highest score. There are other approaches to genotype inversions from SNP data: inveRsion, invClust or PFIDO. However, these approaches have limitations including:

r Rpackage("scoreInvHap") overcomes these difficulties by using a set of reference genotypes from the inversion of interest. The methods is a supervised classifier that genotypes each individual according to their SNP similarities to the reference genotypes across the inverted segment. The classifier in particular uses the linkage desequillibrium (R^2^) between the SNPs and the inversion genoptypes, and the SNPs of each reference inversion-genotypes.

The methods described in the paper "scoreInvHap: Inversion genotyping for genome-wide association studies" by Carlos Ruiz-Arenas et al. (2019)[1] publicly available at PLOS Genetics can be found in release v 1.0.0.

Data and Vignette

The package uses the dataset snpsVCF available at our BRGE group package called brgedata. Vignette can be found here


scoreInvHap stable version can be installed from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))


or from github repository with the latest changes using devtools package:

# Install devtools

# Install scoreInvHap package


In the folder vignettes, scoreInvHap.Rmd contains an example on how to use scoreInvHap.


[1] Ruiz-Arenas, C., Cáceres, A., López-Sánchez, M., Tolosana, I., Pérez-Jurado, L., & González, J. R. (2019). scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genetics, 15(7), [e1008203].

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scoreInvHap documentation built on Feb. 6, 2021, 2 a.m.