Summary: traditional and EM Haseman-Elston analysis No Arguments
Usage -- After typing the command you will be queried as to which phenotype you want to analyze (if you have loaded more than one), and then queried for files to store the text output for the traditional haseman-elston and EM haseman-elston analyses, as well as the filename for the postscript output.
Output -- The traditional and EM haseman-elston output files have the columns:
< position > < beta > < LOD > < t >At the bottom of each of these text output file is a time-stamped summary of the session variables when the command was run. This summary will also list which phenotype was selected and in the case of the EM algorithm, the convergence limit that was used. The postscript output file has a plot of both the traditional and EM results.
Note1: The EM algorithm has been found to have very rare instabilities in large intervals between markers; if there is a sudden peak in the EM plot make sure a similarly shaped peak also appears in the traditional haseman-elston results. (The nonparametric method does not have these instabilities either and can also be used to verify your results.)
Note2: In order to run this command you must have selected more than two pedigrees/pairs -- which shouldn't be a problem since it won't be very significant using any less!