thomaschln/snpclust repository overview

⁠SNPClust

The R package snpclust performs unsupervised feature selection and summarization by selecting SNPs based on principal component analysis (PCA) contributions, and estimating haplotypes of nearby correlated SNPs using the SHAPEIT software.

⁠Installation

⁠Devtools

SNPClust is an R⁠ package that requires the softwares PLINK⁠ and SHAPEIT⁠. Once they are installed, you can open R and use the devtools R package to install the development version from Github:

if (!require(devtools)) install.packages('devtools')
devtools::install_github('ThomasChln/snpclust', build_vignettes = TRUE)

⁠Docker

A Docker image with PLINK, SHAPEIT, and SNPClust installed is available.

docker pull thomaschln/snpclust

⁠Motivation

SNPClust was developed to reclassify systemic autoimmune diseases (SADs) based on genetic markers instead of clinical criteria for the European-funded project PRECISESADS.

It was applied to a genome wide dataset of 379,190 SNPs from 4,212 systemic lupus erythematosus (SLE) patients and 1,221 healthy controls and results were published in PLOS ONE: Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases⁠

It was also used to reproduce the Human Genome Diversity Panel PCA of 300,000 SNPs of 1,000 samples Replication of the principal component analyses of the human genome diversity panel⁠.

⁠Usage

The snpclust function is the main function and can be called on a snpgds file path from the R package SNPRelate⁠. Results can be displayed with several plots. A demo is available in the SNPClust applied to Europeans HTML vignette.

⁠License

This package is free and open source software, licensed under GPL-3.