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sommer (version 1.3)

score.calc: Score calculation for markers

Description

This function is a wrapper from the rrBLUP package to be used when a mixed model including markers to perform GWAS is specified and once the variance components have been estimated the fixed effects are obtained as B= (X'V-X)-X'V-y and the score calculation is obtained with the F statistic as F = Beta^2 / Var(Beta) where Var(Beta) = SSe/(n-p) * [XH-X']-, and quantile value for the beta distribution is calculated as q = (n-p) / (n-p + 1 * F) which once obtained, the -log10 for such value is the score value.

Usage

score.calc(marks,y,Z,X,K,M,Hinv,ploidy,model,min.MAF,max.geno.freq)

Arguments

marks
marker names
y
response variable
Z
incidence matrix of random effects
X
incidence matrix X as full rank from eigen decomposition
K
covariance structure for random effects
M
marker matrix
Hinv
inverse of the phenotypic variance matrix
ploidy
numeric value of ploidy level, i.e. 2
model
model for GWAS
min.MAF
minimum minor allele frequency
max.geno.freq
1 - min.MAF

Value

  • [object Object]

Examples

Run this code
# it works internally in the \code{\link{mmer}} function

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