Description Usage Arguments Value Author(s) References

This function provides the matrix subsitution algorithm. The main idea is to replace the high covariance value entries in the covariance matrix which are produced by family members by a small value (e.g. median covariance).

1 | ```
ms.pca(X, corXresid, threshold, top)
``` |

`X` |
The input data matrix |

`corXresid` |
The correlation of the genotypes after residualization for any evidence of larger scale ancestry. Used to identify close-degree family members in a manner robust to large-scale ancestry. |

`threshold` |
Covariance values of identified family members are set to the threshold. |

`top` |
The number of ancestry scores to obtain. |

`eigenvector` |
Eigenvectors after using the matrix substitution method |

`myeigen` |
The top eigenvalues and eigenvectors |

Yi-Hui Zhou

Computation of ancestry scores with mixed families and unrelated individuals. arXiv:1606.08416.

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