KDPS

KDPS (Kinship Decouple and Phenotype Selection) is an R package designed to resolve cryptic relatedness in genetic studies using a phenotype-aware approach. It retains subjects with relevant traits while pruning related individuals based on kinship or identity-by-descent (IBD) scores.

Features

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

Installation

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

# install.packages("devtools")
# devtools::install_github("UCSD-Salem-Lab/kdps")
install.packages("kdps", repos = c('https://ucsd-salem-lab.r-universe.dev', 'https://cloud.r-project.org'))

Tutorial

You can view the tutorial of the KDPS function with:

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

Example

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)

Documentation

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

Citation

If you use KDPS in your research, please cite:

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

License

This package is released under the MIT License. See LICENSE file for details.