Fast Principal Component Analysis - gc5k/GEAR GitHub Wiki

This function performs fast principal component analysis for genetic data using random sampling.

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Master option: fpca

Options --bfile

Specify the bfile.

--ev

Specify the number of eigenvectors/eigenvalues to print. It is defaulted to 5.

--seed

Specify the seed for sampling.

--prop

Specify the proportion of samples to be used. It is between 0~1, and is defaulted to 1 using all samples.

--adj-var

The genetic relatedness is adjusted by the variance of each locus rather than 2pq.

Examples

gear fpca --bfile test --ev 5 --prop 0.5 --seed 2017 --out test 

The output files are test.eigenvec (eigenvectors) and test.eigenval (eigenvalues).

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