EMMAX:(1)

🌸 NAME 🌸

Okay bestie, listen. This is the manual page for EMMAX:(1) — yes, it's filed under User Commands — and the NAME line literally says:

emmax: - emmax

Minimalist. Iconic. No notes.

✨ SYNOPSIS ✨

emmax [options]

💅 DESCRIPTION 💅

So emmax takes options. The page splits them into Required parameters, Likely essential parameters, and Optional parameters, then it does an error/usage dump and repeats the whole parameter list again. We're gonna keep every fact, every default, every weird little typo vibe. No cap.

🎀 Required parameters 🎀

• -t [tpedf_prefix] — prefix for tped/tfam files.
• -o [out_prefix] — output file name prefix.

💖 Likely essential parameters 💖

• -p [phenof] — 3-column phenotype file with FAMID, INDID at the first two columns, in the same order of .tfam file. Not required only with -K option.
• -k [kinf] — n * n matrix containing kinship values in the individual order consistent to [tpedf].tfam file. [tpedf].kinf will be used if not specified.
• -c [covf] — multi-column covariate file with FAMID, INDID at the first two columns, in the same order of .tfam file.

Also: the original mashes the words Optional parameters right onto the end of that -c line with zero space, so here's the heading it was trying to start:

🌈 Optional parameters 🌈

• -i [in_prefix] — input file name prefix including eigenvectors.
• -d [# digits] — precision of the output values (default: 5).
• -s [start index of SNP] — start index of SNP (default: 0).
• -e [end index of SNP] — end index of SNP (default: #snps).
• -w — flag for writing eigenvalues/eigenvector files.
• -D [delimiters] — delimter string in quotation marks. (Yes, the original really says delimter. We're preserving the lore.)
• -P [# heaer cols in tped] — # of column headers in tped file.
• -F [# heaer cols in tfam] — # of column headers in tfam file.

💀 Error and usage 💀

If you hit an unknown option character, the page says this, literally:

Error : Unknown option character ?Usage: emmax [options] Required
parameters

And then — not me — it repeats the entire parameter list again: same Required parameters, same Likely essential parameters, same Optional parameters, same defaults, same everything. So if you're like "wait, didn't I just read this?", yes bestie, you did. It's a double feature. Scroll up if you need the encore.

There's also this error chilling in the footer:

emmax: invalid option -- '-'

Warning: the original really does say Not required only with -K option, and it really does mention -K without listing -K on its own. That's not me being shady — that's just what the page says.

Source/version: EMMAX:(1), date: June 2013. The footer also had that emmax: invalid option -- '-' error sitting next to it, because of course it did. Bye bestie 💖✨🦋