Summary: maximum likelihood estimate of IBD sharing No Arguments
Usage -- To run the command just type 'estimate'; no arguments are needed. GENEHUNTER will first ask you if you want to analyze your data under the assumption of no dominance variance, or under the assumption of dominance variance where Holman's triangle is applied:
analyze under the assumption of no dominance variance? y/n [n]
The default is to perform the analysis with the assumption of
dominance variance.
GENEHUNTER will then query you for the filenames to store the text and postscript output respectively. You will be alerted if either of the chosen filenames already exist.
Output -- The text file consists of the columns:
< position > < z0 > < z1 > < z2 > < loglike >where the z-values are the calculated maximum likelihood proportions. At the end of the text output is a time-stamped summary of the session settings when the analysis was run. The first postscript output file is a graph of position vs. loglike and the second is a plot of how the maximum likelihood sharing proportions change across the region. The marker names are given along the x-axis and the distance examined in the analysis is given at end of the x-axis (this may be larger than the map distance if you have specified an off-end distance).
Background -- 'estimate' scans the selected map region and identifies regions of significant excess allele sharing.
Note that the LOD score is never negative, because the maximum likelihood solution for z0, z1, and z2 can never be worse than the Mendelian segregation expectation.