mpp_kinship: Compute linkage desequilibrium adjusted kinship

In vincentgarin/mppSim: Functions for simulation in MPP

Compute linkage desequilibrium adjusted kinship

Description

Compute linkage disequilibrium adjusted kinship using the weights computed by the program LDAK. (http://dougspeed.com/ldak/).

Usage

mpp_kinship(gp, weights = NULL, power = -1, mk.sel = NULL)

Arguments

gp	gpData object with elements geno coded 0 1 2.
weights	Two columns data.frame containing the marker identifiers and the weights marker weights. For example the weights obtained with the LDAK program (see LDAK_weights). By default, the kinship matrix is computed unweighted or all weights are equal to 1, which correspond to the Astle and Balding kinship matrix
power	Numerical value specifying the value of the parameter for marker scores standardization. The column of the marker matrix (X.j) are multiplied by var(X.j)^(power/2). It correspond to alpha in the formula .Default = -1.
mk.sel	Character vector specifying a list of marker to use for the kinship matrix computation. By default, the function use all markers of the gpData object.

Details

The formula used to compute the kinship is the following:

(1/sum(wj)) [sqrt(wj)(Xj - 2pj)][sqrt(wj)(Xj - 2pj)]'/[(2pj(1-pj))^alpha]

The results return by the function are two times the results given by LDAK using –calc-kins-direct.

Value

Return:

K	Kinship matrix computed with the LDAK weights.

Author(s)

Vincent Garin

References

Astle, W., & Balding, D. J. (2009). Population structure and cryptic relatedness in genetic association studies. Statistical Science, 451-471.

Speed, D., Hemani, G., Johnson, M. R., & Balding, D. J. (2012). Improved heritability estimation from genome-wide SNPs. The American Journal of Human Genetics, 91(6), 1011-1021.

vincentgarin/mppSim documentation built on Oct. 11, 2024, 3:18 p.m.