karim {ggmix} | R Documentation |
Karim's Simulated Data
Description
A simulated dataset with a kinship matrix
Usage
karim
Format
A list with 6 elements:
- b
vector of length 1000 representing the true regression coefficients. 10 non-zero coefficients, the rest are 0.
- kin1
the true kinship matrix
- s.g
polygenic variance, set to be 1.26
- s.e
error variance, set to be 1
- h.tot
the total trait heritability. Set to be 60 of genotypes of dimension 600 x 1000 SNPs, with approximately 800 common and 200 rare SNPs
Details
If you simulate data using the scenario provided in the example, then the QTL heritability of y will be 8 of the trait’s total heritability), and the trait total heritability is set to be 60
Examples
data(karim)
# Simulate a response using the genotype matrix and the kinship matrix
Phi <- 2 * karim$kin1
intercept <- 1
P <- MASS::mvrnorm(1, rep(0,600), karim$s.g * Phi)
y <- intercept + karim$G %*% karim$b + P + rnorm(600,0,karim$s.e)
[Package ggmix version 0.0.2 Index]