kdps

Remove related subjects based on kinship matrix as well as subject phenotype

https://github.com/ucsd-salem-lab/kdps

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Remove related subjects based on kinship matrix as well as subject phenotype

README.Rmd

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output: github_document
---

# 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:

```{r,eval=FALSE}
# install.packages("devtools")
devtools::install_github("UCSD-Salem-Lab/kdps")
```

## Tutorial

You can view the tutorial of the KDPS function with:

```{r,eval=FALSE}
vignette("kdps-intro", package = "kdps")
```

## Example

```{r,eval=FALSE}
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](https://ucsd-salem-lab.github.io/kdps/)
- [Getting Started with KDPS](https://ucsd-salem-lab.github.io/kdps/articles/kdps-intro.html)
- Function reference: `?kdps`

## Citation

If you use KDPS in your research, please cite:

> Wanjun Gu, Jiachen Xi, Steven Cao, Rany M. Salem. *Kinship Decouple and Phenotype Selection (KDPS)*. Manuscript in preparation

## License

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

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