ms.pca {PCFAM}

The matrix substitution approach

Description

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).

Usage

ms.pca(X, corXresid, threshold, top)

Arguments

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.

Value

eigenvector

Eigenvectors after using the matrix substitution method

myeigen

The top eigenvalues and eigenvectors

Author(s)

Yi-Hui Zhou

References

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