Summary: maximum likelihood QTL variance estimation 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 a files to store the text and postscript output.
Output -- The text output file has the format:
< position > < LOD > < sigsq0 > < sigsq1 > < sigsq2 >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 the convergence limit that was used. The postscript output file is a plot of position vs. LOD.
Note: This EM-based algorithm has been found to have very rare instabilities in large intervals between markers; if there is a sudden peak in the plot you can verify it by checking it against the results of the nonparametric method, which is not subject to the same instabilities.