Description Usage Arguments Value
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.
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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 |
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.
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