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kdps  

Kinship Decouple and Phenotype Selection (KDPS)
View on CRAN: Click here


Download and install kdps package within the R console
Install from CRAN:
install.packages("kdps")

Install from Github:
library("remotes")
install_github("cran/kdps")

Install by package version:
library("remotes")
install_version("kdps", "1.0.0")



Attach the package and use:
library("kdps")
Maintained by
Wanjun Gu
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-07-22
Latest Update: 2025-07-22
Description:
A phenotype-aware algorithm for resolving cryptic relatedness in genetic studies. It removes related individuals based on kinship or identity-by-descent (IBD) scores while prioritizing subjects with phenotypes of interest. This approach helps maximize the retention of informative subjects, particularly for rare or valuable traits, and improves statistical power in genetic and epidemiological studies. KDPS supports both categorical and quantitative phenotypes, composite scoring, and customizable pruning strategies using a fuzziness parameter. Benchmark results show improved phenotype retention and high computational efficiency on large-scale datasets like the UK Biobank. Methods used include Manichaikul et al. (2010) <doi:10.1093/bioinformatics/btq559> for kinship estimation, Purcell et al. (2007) <doi:10.1086/519795> for IBD estimation, and Bycroft et al. (2018) <doi:10.1038/s41586-018-0579-z> for UK Biobank data reference.
How to cite:
Wanjun Gu (2025). kdps: Kinship Decouple and Phenotype Selection (KDPS). R package version 1.0.0, https://cran.r-project.org/web/packages/kdps. Accessed 12 Mar. 2026.
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