NAME¶
ilink - GEMINI optimization procedure to find a locally optimal value of the
theta vector of recombination fractions
SYNOPSIS¶
ilink [
options]
ipedfile.dat pedfile.dat
DESCRIPTION¶
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
system.
OPTIONS¶
There might be options but I did not found any information about them. Please
foreward any information about them to <tille@debian.org>
SEE ALSO¶
linkmap(1),
lodscore(1),
mlink(1),
unknown(1).
Word-Wide-Web:¶
http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
AUTHOR:¶
Alejandro Schaeffer <schaffer@helix.nih.gov> and others
This manual page was written by Andreas Tille <tille@debian.org>, for the
Debian GNU/Linux system (but may be used by others).