ILINK(1)

📦 version 4.1P-fix100, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

ok so bestie, welcome to ilink, living under the General Commands Manual umbrella ✨

🌸 NAME 🌸

ilink — the GEMINI optimization procedure that goes hunting for a locally optimal value of the theta vector of recombination fractions 🧬💅

🦋 SYNOPSIS 🦋

ilink [options] ipedfile.dat pedfile.dat

✨ DESCRIPTION ✨

okay so real talk, this manual page is gonna document the ilink command briefly. And ngl, the vibe here is that this is a very raw attempt at a manpage, because the Debian GNU/Linux distribution requires every program to have one. So like… it exists. If you wanna make it better, any enhancement would be greatly apreciated 🫶 (that's a direct quote, spelling and all, periodt).

ilink is part of the fastlink software package, iykyk.

So what does it actually DO? ILINK uses the GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions. And here's the tea: if you use the default scripts produced by lcp, your initial guess for theta is .1 in every dimension. GEMINI then evaluates each theta by its likelihood, seeking out theta vectors that have a higher pedigree likelihood. It's giving main character energy for genetic linkage analysis fr fr 🔥

Now the GEMINI procedure has multiple iterations. Each iteration corresponds to one line of output. Each iteration includes multiple likelihood function evaluations. And 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.

And a lil detail that matters: in the first iteration, Phase I only evaluates the likelihood at the initial candidate theta. no cap 🫡

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. But wait — if maletheta and femaletheta are allowed to differ (that's sexdif set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). And estimating other parameters (with fitmodel set to true) can also increase the number of dimensions. math is mathing 📐💀

Wanna 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 honestly, the author did not found any information about them 🙈
Please foreward any information about them to <tille@debian.org> — they're literally asking, be a hero 🫶

👑 SEE ALSO 👑

🌈 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). slay 💜

and that's the whole thing bestie!! this page is from April 15, 2003, brought to you by the Debian GNU/Linux system ✨ go forth and optimize those thetas 🧬💖🦋

📦 where this page comes from