qtl2pleio

"qtl2pleio" is an R package to address the complexities of understanding the genetic architecture of complex traits, significantly when leveraging the high mapping resolution of multi parental populations and the capability to measure a vast array of phenotypes. Recognizing the challenge of distinguishing between pleiotropy and close linkage when multiple traits map to the same genomic region, qtl2pleio extends the method initially proposed by Jiang and Zeng (1995) to encompass situations involving more than two alleles.

Key Features and Functionalities:

- Enhanced Pleiotropy Testing: qtl2pleio allows for testing pleiotropy with a pair of traits and extends this methodology to cases with more than two alleles, offering a more nuanced analysis of the genetic underpinnings of complex traits.

- Accounting for Population Structure: The package incorporates polygenic random effects to address population structure, ensuring that the analysis accommodates underlying genetic diversity within the studied populations.

- Statistical Significance via Parametric Bootstrap: To determine the statistical significance of findings, qtl2pleio employs a parametric bootstrap approach, providing a robust framework for evaluating the results.