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KDPS (Kinship Decouple and Phenotype Selection) is an R packagedesigned to resolve cryptic relatedness in genetic studies using aphenotype-aware approach. It retains subjects with relevant traitswhile pruning related individuals based on kinship oridentity-by-descent (IBD) scores.

• Prioritizes individuals with key phenotypes (categorical or numeric)
• Supports phenotype ranking and composite scoring
• Customizable pruning usingfuzziness parameter
• Efficient on biobank-scale datasets like UK Biobank
• Compatible with both kinship and phenotype file formats

You can install the development version of KDPS from GitHub with:

# install.packages("devtools")devtools::install_github("UCSD-Salem-Lab/kdps")

You can view the tutorial of the KDPS function with:

vignette("kdps-intro",package="kdps")

library(kdps)phenotype_file= system.file("extdata","simple_pheno.txt",package="kdps")kinship_file= system.file("extdata","simple_kinship.txt",package="kdps")kdps_results= kdps(phenotype_file=phenotype_file,kinship_file=kinship_file,fuzziness=0,phenotype_name="pheno2",prioritize_high=FALSE,prioritize_low=FALSE,phenotype_rank= c("DISEASED1","DISEASED2","HEALTHY"),fid_name="FID",iid_name="IID",fid1_name="FID1",iid1_name="IID1",fid2_name="FID2",iid2_name="IID2",kinship_name="KINSHIP",kinship_threshold=0.0442,phenotypic_naive=FALSE)head(kdps_results)

• KDPS Documentations
• Getting Started withKDPS
• Function reference:?kdps

If you use KDPS in your research, please cite:

Wanjun Gu, Jiachen Xi, Steven Cao, Rany M. Salem. (2025).KinshipDecouple and Phenotype Selection (KDPS): a tool for phenotype-awaredecoupling of related subjects.. Brief. Bioinform. 26,bbaf561.

This package is released under the MIT License. SeeLICENSE file fordetails.