PERMUTESMOOTH(1)

✨ permuteSmooth ✨

okay bestie, welcome to permuteSmooth, a little icon from the permuteSmooth (VCF statistics) corner of the world 💖 she's a statistics girlie, she's a vcflib girlie, and she's here to help you out. let's get into it 🫶

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💅 NAME 💅

permuteSmooth — no cap, that's the whole name, that's her government name, periodt.

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🎀 SYNOPSIS 🎀

permuteSmooth -s wcFst.smooth.txt -f wcFst.txt -n 5 -s 1

yes she used -s twice in her own example, and yes we love her for it 💀 iconic behavior, we don't question it.

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🌸 DESCRIPTION 🌸

permuteSmooth is a method for adding empirical p-values smoothed wcFst scores. that's the vibe. that's the assignment. she takes your scores and she gives them p-values, empirically, through permutations 🦋

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✨ OPTIONS ✨

💖 Required 💖

• file / f — argument: original wcFst data. this is your O.G. file, the before-picture, the source material 📂
• smoothed / s — argument: smoothed wcFst data. this is the after, the glow-up version, the smoothed one 🧖‍♀️
• format / y — argument: [swcFst, segwcFst]. pick your format bestie, those are the options, no others 💅

🌈 Optional 🌈

• number / n — argument: the number of permutations to run for each value [1000]. default is one thousand, she will absolutely run one thousand of them 🌀
• success / u — argument: stop permutations after 's' successes [1]. once she's got her wins, she can stop, and the default is 1 🏆
• success / x — argument: number of threads [1]. yes, the label says success again, and no, that's not a typo we're allowed to fix, so here it is exactly as written 🙈 the default is 1 thread.

not me noticing two options both labeled success up there 👀 we reproduce the manual exactly as it is, quirks and all, because that's the rule and the rule is sacred 💖

📊 OUTPUT 📊

permuteSmooth will append three additional columns:

1. The number of successes
2. The number of trials
3. The empirical p-value

Type:</purl> statistics — that's her category, that's her lane, she stays in it 🎀

(that was supposed to say <purple>**Type:**</purple> — we're all human, and we're all doing our best 🫶) Type: statistics.

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🦋 EXIT VALUES 🦋

• 0 — Success 🎉 she ate and left no crumbs
• not 0 — Failure 😭 something went sideways, and no amount of slay can fix it

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🌟 SEE ALSO 🌟

• vcflib(1) — her whole family, go say hi 👑

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🎀 OTHER 🎀

the important-but-official bits live here, bestie. legal girlies, this one's for you 💜

💜 LICENSE 💜

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

MIT licensed means you can use it, share it, remix it — just keep the credit, because giving credit is main character energy and stealing credit is not 💅

👑 AUTHORS 👑

Erik Garrison and vcflib contributors.

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and that's the whole page, bestie 🫶 this was permuteSmooth (vcflib), written up with love, and if you ever forget who made her: Erik Garrison, the vcflib contributors, and Pjotr Prins, forever and always 💖✨🎀