compute.weights: Compute/create matrix with genotype weights

In RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

Description

Compute/create matrix with genotype weights

Usage

compute.weights(G, weights)

Arguments

G	matrix of genotypes (genetic variants as columns, individuals as rows) as output by the Get.G function.
weights	optional numeric vector of genotype weights. If this option is not specified, the beta distribution is used for weighting the variants, with each weight given by w_i = dbeta(f_i, 1, 25)^2, with f_i the minor allele frequency (MAF) of variant i. This default is the same as used by the SKAT package. This vector is used as the diagonal of the m \times m matrix W, with m the number of variants.

Details

If the weights parameter (a numeric vector) is given, this function will return a matrix with that vector as the diagonal. If the weights parameter is not given (equal to NULL) the genotype weights will be calculated using the beta distribution (see the explanation of the weights parameter).

Value

Matrix with genotype weights.

Author(s)

Karim Oualkacha, Lennart C. Karssen

RVPedigree documentation built on May 29, 2017, 10:19 p.m.