@@ -112,7 +112,11 @@ There are two ways to install required R packages for this analysis;
For Projected Leaf Area (PLA), we calculated Best Linear Unbiased Estimates (BLUEs) for genotypic means, used as phentoypes in the BLUP models using 'BLUES.R' script. The BLUEs for Phi-PSII are already available from Van Rooijen 2017.
# 3- Genotype Dataset Preparation
Genotype data of the 360 natural accessions in the core set of the _Arabidopsis thaliana_ HapMap population, representing its global diversity, was obtained using Affymetrix 250k SNP array (Zhang and Borevitz, 2009;Baxter et al., 2010). The raw genotypes were in plink binary format and after MAF and LD filtering, recoded into compound genotypes using and subsequently, converted into allele count matrix (M) using 'make_M_matrix.sh'.
# 4- Prior groups of genes (GO/COEX)
# 4- Prepare Genomic Relationship Matrix (GRM)
- A GRM (G) was contructed based on all markers
- and each GO/COEX groups
The M matrix was centered and scaled to calculate Genomic Relationship Matrix (GRM) using Allele Frequency based method, proposed by (VanRaden, 2008).
Sets of GO terms and coexpressed clusters of genes were loaded and GRMs were constructed for each group such that for each GO/COEX group; a GRM was constructed based on only of those markers within that set of genes and another was constructed based on rest of all markers.