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KDPS

KDPS (Kinship Decouple and Phenotype Selection) isan R package designed to resolve cryptic relatedness in genetic studiesusing aphenotype-aware approach. It retains subjectswith relevant traits while pruning related individuals based on kinshipor identity-by-descent (IBD) scores.

Features

• Prioritizes individuals with key phenotypes (categorical ornumeric)
• 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

Installation

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

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

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

• KDPSDocumentations
• GettingStarted with KDPS
• Function reference:?kdps

Citation

If you use KDPS in your research, please cite:

Wanjun Gu, Jiachen Xi, Steven Cao, Rany M. Salem.KinshipDecouple and Phenotype Selection (KDPS). Manuscript inpreparation

License

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