gr.pca: The geometric rotation approach

In PCFAM: Computation of Ancestry Scores with Mixed Families and Unrelated Individuals

Description

This algorithm rotates scaled genotypes among family members so that they are mutually orthogonal.

Usage

gr.pca(data.input, index.family, myfam, weight, top, family.size, inflation)

Arguments

data.input	Input dataset, each row is for a genetic feature (SNP), each column is for individual. Data are typically number of minor alleles, possibly imputed.
index.family	Index vector to indicate the family id of each individual.
myfam	This value comes directly from the output of findfamilies().
weight	Weight is 0 by default. This is a deprecated weight value that can be used to control the amount of rotation performed. A weight of zero performs full orthogonalization, while a weight of 1 keeps the data unchanged.
top	The number of eigenvectors to be used.
family.size	The number of members in each family. Used to determine rotation angles.
inflation	The inflation of the data value is 0 under default. Deprecated.

Value

data.new	The new datamatrix after the geometric rotation
topPCs	The top eigenvectors
topEigenvalue	The top eigenvalues.

Author(s)

Yi-Hui Zhou

References

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

PCFAM documentation built on May 2, 2019, 2:37 a.m.