Example PCA, PERMANOVA and PERMDISP analysis1 years ago
Description of the data | Install package smartsnp (use one option) | Load package | Create group factor | Run smart_pca | Run smart_permanova | Run smart_permdisp | Run smart_mva
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Projecting ancient samples1 years ago
Install package smartsnp | Downloading the data | Select subsets of individuals with convertf | Merging ancient with modern data using mergeit | Running smartpca | Plotting the results using ggplot2
Using VCF and PLINK formatted files with smartsnp5 years ago
Download a small example VCF | VCF to PLINK (.bed) | PLINK to raw genotype (.traw) | VCF to raw genotype (.traw) | Running smartpca