CNVKIT_BINTEST(1)

💖 CNVKIT_BINTEST(1) 💖

okay bestie, welcome to cnvkit_bintest — it's a User Command, it lives in section 1 of the manual, and it is literally the "Test for single-bin copy number alterations." vibe. no cap. 🧚

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✨ NAME ✨

cnvkit_bintest — Test for single-bin copy number alterations.

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🌸 DESCRIPTION 🌸

so the way this works is, you run it like this:

usage: cnvkit.py bintest [-h] [-s FILENAME] [-a ALPHA] [-t] [-o OUTPUT]

       cnarray

that's the whole shape of it. <lavender>cnarray</lavender> is the main character here, everything else is optional garnish. 🎀

🌈 positional arguments 🌈

• cnarray — this is your bin-level log2 ratios file, a .cnr file, and it's gotta be the kind that comes out of the fix command. that's the whole point, that's what we're testing. 💅

🦋 options 🦋

• -h, --help — shows you this help message and then dips. classic. shows help, exits, we love a clean exit. ✨
• -s FILENAME, --segment FILENAME — your segmentation calls, a .cns file, aka the output of the segment command. that's where these calls came from, iykyk. 🍓
• -a ALPHA, --alpha ALPHA — the significance threshold. [Default: 0.005] — yeah, that's the default, she's strict. 👑
• -t, --target — test target bins only, and just straight up ignore the off-target bins. like, not even a glance. 🙈
• -o OUTPUT, --output OUTPUT — output filename. give your results a name, they deserve one. 💜

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ngl bestie, -a is spelled "threhold" in the original and honestly? iconic of it. we keep it, we don't fix it, we simply respect the typo. 💀

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💫 SEE YA 💫

that's the whole page, fr fr. this gorgeous thing is cnvkit.py bintest 0.9.10, dated July 2023, and it signs off as CNVKIT_BINTEST(1). periodt. 🫶💖