Genomic Analysis ToolsThese analysis tools use the R package rrBLUP version 4.2
rrBLUP is available at The Comprehensive R Archive Network
|y = X β + Ζ g + ε||
y = observations|
Z = Design matrix for the random effects
X = Design matrix for fixed effects
Principal components can also be added as a fixed effect.
Genome Wide Association (GWAS)
- R function GWAS(pheno, geno, fixed="trial", K=mrkRelMat, n.PC=model_opt1, P3D=model_opt2)
- method (EMMAX Kang et al. 2010) - variance components are estimated by REML only once, without any markers in the model. This method is faster but can underestimate significance.
- method (EMMA with REML Kang et al. 2008) - variance components are estimated by REML for each marker separately.
- The dashed line in the Manhattan plot indicates a False Discovery Rate (FDR) of 0.05. When there are no significant loci the dashed line is omitted.
- Markers that are not mapped are assigned to chromosome 0 and a position that increments by 10
- R function kin.blup(data, "geno", "pheno", K=mrkRelMat, fixed="trial")
- An additive relationship matrix is used for K to creates the model (G = K Vg).
- In the prediction set the trait values, if any, are set to missing.