VarQTL v1.01
Detecting loci changing trait (co)variances. Essentially this code goes through every marker and tests whether two genotypes differ in single-trait variance (canalization locus) or the shape / size / orientation of multi-trait covariance structure (different trait in the same environment: locus relaxing genetic constraint; the same trait in different environment: locus affecting genotype-by-environment interaction).
1. Please cite: Lee, C-R, JT Anderson, T Mitchell-Olds. 2014. Unifying genetic canalization, genetic constraint, and genotype-by-environment interaction: QTL by genomic background by environment interaction of flowering time in Boechera stricta. PLoS Genetics 10(10): e1004727
2. Currently it can only work on crosses with two distinct genotypes (such as recombinant inbred line or double haploid line). The two marker genotypes should be coded AA and BB.
3. For single trait canalization, use the function VarQTL.BFtest (Brown–Forsythe test: this requires the R package "lawstat").
4. For multi-trait covariance relationship, use VarQTL.Krzanowski (for the Krzanowski index), VarQTL.covGmaxangle (for angle between PC1), or VarQTL.BoxM (for Box M value).