lodscore(1) [linux man page]
LODSCORE(1) General Commands Manual LODSCORE(1) NAME
lodscore - compares likelihoods at locally optimal theta SYNOPSIS
lodscore [options] ipedfile.dat pedfile.dat DESCRIPTION
This manual page documents briefly the lodscore 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. lodscore is part of the fastlink software package. Lodscore compares -2log(likelihood) at the locally optimal theta to -2log(likelihood) at a theta that is 1/2 in every component (i.e. each locus unlinked to all the rest). In LINKAGE ILINK more likelihood function evaluations are done after the last printed iteration line, but these likelihood function evaluations are unnecessary (see paper2.ps from the fastlink-doc Debian package for more details). 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
ilink(1), linkmap(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). April 15, 2003 LODSCORE(1)
Check Out this Related Man Page
ILINK(1) General Commands Manual ILINK(1) 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 esti- mates 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 male- theta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). Esti- mating 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). April 15, 2003 ILINK(1)