ms.pca {PCFAM} | R Documentation |
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).
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.