emma.kinship {emma}R Documentation

IBS Kinship matrix generation

Description

Generates and returns an IBS kinship matrix from snp data

Usage

  emma.kinship(xs, method = c("additive","dominant","recessive"), use = c("all","complete.obs","pairwise.complete.obs"))

Arguments

xs a m by t matrix, where m is number of indicator variables (or snps), and n is the number of strains
method a character string representing the effect of heterozygous alleles.
use a character string giving a method for computing kinship coefficient in the presence of missing values. This must be (an abbreviation of) one of the strings "all", "complete.obs" or "pairwise.complete.obs"

Details

The IBS kinship matrix is computed as simple pairwise genotype similarities. Based on the one of additive, dominant, recessive models for heterozygous alleles. If "all" option is used, the missing alleles are used based on the minor allele frequencies. If "complete.obs" option is used, all the SNPs containing missing alleles are discarded. If "pairwise.complete.obs" option is used, only the missing alleles are discarded, but it may disrupt the positive semidefiniteness of the kinship matrix.

Value

A t by t matrix containing kinship coefficients between every pair of strains.

Author(s)

Hyun Min Kang h3kang@cs.ucsd.edu

References

Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, and Eskin E, Efficient Control of Population Structure in Model Organism Association Mapping, Genetics 178:1709-1723, 2008

See Also

emma.ML.LRT,emma.REML.t,emma.MLE,emma.REMLE

Examples

  ## Not run: 
    ## Load data
    data(emmadat)

    ## Generate kinship matrix
    K <- emma.kinship(emmadat$xs,"additive","all")

    ## Run EMMA
    rs <- emma.REML.t(emmadat$ys,emmadat$xs,K)

    ## return p-values
    rs$ps
  ## End(Not run)

[Package emma version 1.1.2 Index]