The "rNeighborQTL" package provides a set of functions to perform a genome scan of neighbor QTL effects.
Theoretical background is described in Sato, Takeda & Nagano (2020).
See vignette("rNeighborQTL") for how to use this package.
Neighbor QTL is an extended method of single-marker regression.
Taking conditional genotype probabilities from r/qtl package, the rNeighborQTL package performs an interval mapping of neighbor genotypic identity.
Alternative to QTL mapping, rNeighborGWAS package is also available for genome-wide association studies (GWAS) via CRAN at https://cran.r-project.org/package=rNeighborGWAS.
Sato Y, Yamamoto E, Shimizu KK, Nagano AJ (2019) Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory on Arabidopsis thaliana. bioRxiv https://doi.org/10.1101/845735
Sato Y, Takeda K, Nagano AJ (2020) Neighbor QTL: an interval mapping method for quantitative trait loci underlying neighbor effects. bioRxiv https://doi.org/10.1101/2020.05.20.089474