| gr.pca {PCFAM} | R Documentation |
The geometric rotation approach
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.