| checkXy | Check input values. |
| gensim | Genetic similarity matrix for scaled genotype X. |
| half.inv | Half-inverse matrix operation |
| heritability | Estimate heritability. |
| HPQTL2 | HPQTL2 |
| normalize.matrix | Normalize Matrix |
| scan.lm | One Locus Scan for Linear Model. |
| scan.lmm | One Locus Scan for Linear Mixed Model. |
| scan.loco | One Locus Scan for for Leave One Chromosome Out Method. |
| scanoneTemplate | Create R/qtl scanone object |
| scan.pomo | One Locus Scan for Project One Marker Out Method. |
| scan.pomoloco | One Locus Scan for Project One Marker Out Method. |
| sim.geno.f2 | Simulate F2 cross genotypes |
| sim.pheno | Simulate phenotype with the given background heritability,... |
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