QTLRel Package: functionalities (2)

9. gls: Generalized Least Square Estimates, Obtain estimates using generalized least squares (gls)

10. hapSim: Generate Genotypic Data, Simulate gametic data from a pedigree.

The pedigree should be in the same format as an output of pedRecode.

11. ibs: Estimate Jacquard condensed identity coefficients, Estimate Jacquard condensed coefficients by identity-by-state (IBS) from genotypic data.

12. kinship: Calculate kinship coefficients, Calculate kinship coefficients from a pedigree.

13. lodci: Estimate LOD Support Intervals.

In case of multiple peaks on chromosome, a peak has to satisfy: a) above the threshold cv; b) drops, e.g., 3 LOD on both sides except chromosome ends. So if two peaks close to each other but LOD between them doesn't drop, e.e., 3 LOD, only one of them is considered.

14.mAIC: multiple QTL AIC, Multiple QTL model selection by AIC criterion.

Makes use of "Haley-Knott" method (Haley and knott 1992) if prdat is an object from genoProb.

15. miscEx: Genotype data, phenotype data, genetic map and pedigree.

AIL F8 data include the following:

gmF8: a list with elements inbreeding coefficients "id", additive genetic matrix "AA", dominance genetic matrix "DD" and other genetic matrices.

pedF8: pedigree data.

gmapF8: genetic map.

gdatF8: genotype data.

pdatF8: phenotype data.

usage data(miscEx)

16. misFct: A collection of other functions that are not needed by users.