PCFAM-package: Computation of ancestry scores with mixed families and...

Description Details Author(s) References Examples

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

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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)

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