ilink - GEMINI optimization procedure to find a locally optimal value
of the theta vector of recombination fractions
ilink [options] ipedfile.dat pedfile.dat
This manual page documents briefly the ilink command. In fact this is
a very raw intend to provide a manpage because the Debian GNU/Linux
distribution requires each program to have a manpage. Any enhancement
would be greatly apreciated.
ilink is part of the fastlink software package.
ILINK uses the GEMINI optimization procedure to find a locally optimal
value of the theta vector of recombination fractions. If you use the
default scripts produced by lcp, your initial guess for theta is .1 in
every dimension. GEMINI evaluates each theta by its likelihood,
seeking to find theta vectors that have a higher pedigree likelihood.
The GEMINI procedure has multiple iterations. Each iteration
corresponds to one line of output. Each iteration includes multiple
likelihood function evaluations. Each iteration has two phases. In
Phase I GEMINI seeks to improve the current best theta. In Phase II,
GEMINI estimates the gradient of the likelihood with respect to the
current best theta vector. In the first iteration, Phase I only
evaluates the likelihood at the initial candidate theta.
When ILINK prints out a line such as: maxcensor can be reduced to
-32767, it has completed the first likelihood function evaluation. On
long runs, this fact can be used to estimate running time. A reasonable
rough estimate for the number of function evaluations is 10*(number of
dimensions of theta vector). The number of dimensions of the theta
vector is one fewer than the number of loci in most cases. If maletheta
and femaletheta are allowed to differ (sexdif is set to 1), then the
number of dimensions doubles to 2 * (number of loci - 1). Estimating
other parameters (with fitmodel set to true) can also increase the
number of dimensions.
To learn more about ilink it might be useful to read the file
/usr/share/doc/fastlink/README.ILINK if you have a Debian GNU/Linux
There might be options but I did not found any information about them.
Please foreward any information about them to <email@example.com>
linkmap(1), lodscore(1), mlink(1), unknown(1).
Alejandro Schaeffer <firstname.lastname@example.org> and others
This manual page was written by Andreas Tille <email@example.com>, for
the Debian GNU/Linux system (but may be used by others).
April 15, 2003