| PCFAM-package {PCFAM} | R Documentation |
Computation of ancestry scores with mixed families and unrelated individuals
Description
This package provides ancestry scores based on genotype data, and is robust to the presence of close-degree family members. Four main novel algorithms are represented: (i) Geometric rotation (within-family data orthogonalization); (ii) matrix substitution based on the decomposition of a target family-orthogonalized covariance matrix; (iii) covariance-preserving whitening, retaining covariances between unrelated pairs while orthogonalizing family members (Note: the function perfectwhiten generates a new dataset which keeps the same covariance structure as the original set); (iv) using family-averaged data to obtain loadings for projection of family members.
Details
| Package: | PCFAM |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2016-10-11 |
| License: | GPL 2 |
| LazyLoad: | yes |
Author(s)
Yi-Hui Zhou
Maintainer: Yi-Hui Zhou <yihui_zhou@ncsu.edu>
References
Computation of ancestry scores with mixed families and unrelated individuals. arXiv:1606.08416
Examples
X <- matrix(rbinom(1000*20,2,0.4),1000,20)
X[,1]=X[,2]*0.9
X=rowscale(X)
Xresid=residualize(X)
corXresid=cor(Xresid)
myfam=findfamilies(corXresid,0.1)
K=3
myms.pca=ms.pca(X,corXresid,0.1,K)
familyave.result=familyave(X,myfam,top=K)