Individual i is a recombinant w.r.t. parent p , if i inherits the A allele from one chromatid of p and the B allele from the other chromatid of p . On the same chromosome, and they are close for small values. 1 Morgan means 1 expected crossover Relationship between Morgans and Megabases is poorly understood. Mapping Functions Mapping functions convert from to x and back. Higher likelihood is better.
Thresholds depend on the bad consequences to society from false negatives and false positives.
Use the best choice for hypothesis . This is very useful for multiple data sets. Always do two locus analysis between disease and marker probe of known position. Interested in lodscores above 1 or 2. Two-stage scans can reduce lab costs.