snpclust: snpclust

In ThomasChln/snpclust: SNP Feature Summarization for Unsupervised Clustering

Description

SNPClust performs PCA-based SNP selection and haplotype summarization of nearby correlated SNPS in linear complexity using the SHAPEIT software. Features are then weighted by pricipal component rank and contributions.

Usage

snpclust(
  gds,
  bed_paths,
  n_axes = 100,
  n_cores = 1,
  only_pca = FALSE,
  keep_tmp = FALSE,
  ...
)

Arguments

gds	Path of Genomic Data Structure file
bed_paths	Paths of PLINK binary files. If missing, files are generated with the gds file.
n_axes	Number of principal components to consider
n_cores	Number of cores to use
only_pca	Logical, compute only PCA and exit
keep_tmp	Logical, keep temporary objects
...	Passed to snprelate_qc

Value

List of slots: gdata: GenotypeData object of the quality controlled gds, qc: details about the quality control applied, pca: PCA applied to the quality controlled gds, peaks: list of SNP IDs selected in each principal component, features: matrix of selected SNPs and estimated haplotypes, features_pca: PCA applied to the features.

ThomasChln/snpclust documentation built on June 11, 2020, 4:27 p.m.