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.
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)A Docker image with PLINK, SHAPEIT, and SNPClust installed is available.
docker pull thomaschln/snpclust
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.
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.
This package is free and open source software, licensed under GPL-3.