PERMUTEGPAT++(1)

💖 PERMUTEGPAT++ — the permuteGPAT++ era 💖

okay bestie, buckle up, because this one is a whole little icon in the vcflib cinematic universe. it's called permuteGPAT++, it lives in the permuteGPAT++ (VCF phenotype) section of the manual, and it is genuinely so useful once you get it. let's go 🫶

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✨ NAME ✨

permuteGPAT++ — literally just that. that's the name, that's the program, that's the vibe. 💅

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🦋 SYNOPSIS 🦋

permuteGPAT++ -f gpat.txt -n 5 -s 1

that's it, that's the whole invocation. three flags and you're off. 🌸

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💜 DESCRIPTION 💜

so like, permuteGPAT++ is a method for adding empirical p-values to a GPAT++ score. that's the entire job description. no cap, that's what it does. it takes your score and it gives it the p-value treatment, empirically. periodt. ✨

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🎀 OPTIONS 🎀

first things first, a heads up from the source itself:

Currently permuteGPAT++ only supports wcFst, but will be extended.

so rn it's a wcFst girlie, and more is coming later. noted. 💖

🌈 OUTPUT

permuteGPAT++ will append three additional columns to your stuff. three! new! columns! and they are:

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

obsessed, honestly. the receipts are right there in the output. 🧚

🍓 the actual flags

• -f (file) — the argument is the input file. your data goes here. that's the whole thing. 📁
• -n (number) — the argument is the number of permutations to run for each value. default is [1000]. so if you don't say anything, it's doing a thousand of them. a thousand! 🔥
• -s (success) — the argument is: stop permutations after s successes. default is [1]. so it bails out once it's seen s wins. 🏆

Type: phenotype — that's the type of this whole operation, iykyk.

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💀 EXIT VALUES 💀

• 0 — Success. slay. ✨
• not 0 — Failure. 💀

that's the binary, bestie. either it ate or it didn't.

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🌸 SEE ALSO 🌸

• vcflib(1) — go say hi to the family, this one runs with the vcflib crowd. 🫶

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⭐ OTHER ⭐

nothing extra to report here, it's just the vibe section. moving on. 💅

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👑 LICENSE 👑

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

MIT licensed, so it's free, it's open, it's generous. respect. 🎀

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🌈 AUTHORS 🌈

Erik Garrison and vcflib contributors. absolute legends, no further questions. 👑

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okay so that's the whole page, and if you made it to the end: congrats, you now officially understand permuteGPAT++. this one ships out of the vcflib collection, so when you see permuteGPAT++ (vcflib) stamped on it, that's your people. go run it on your phenotype data and let it cook. bye bestie, mwah 💖🦋🌸