CNVKIT_GENEMETRICS(1)

✨ CNVKIT_GENEMETRICS ✨

okay bestie, welcome to the cnvkit_genemetrics page from the User Commands section of the manual (that's section 1, iykyk) 💅

🌸 NAME 🌸

cnvkit_genemetrics — the way it just identifies targeted genes with copy number gain or loss 🧬✨ periodt.

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🎀 DESCRIPTION 🎀

okay so the usage goes a little something like this:

cnvkit.py genemetrics [-h] [-s SEGMENT] [-t THRESHOLD] [-m MIN_PROBES] [--drop-low-coverage] [-y] [-x {m,y,male,Male,f,x,female,Female}] [-o FILENAME] [--mean] [--median] [--mode] [--ttest] [--stdev] [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] filename

she's long, she's detailed, she's serving 💖

🫶 positional arguments:

• filename — this is your processed sample coverage data file, the *.cnr one, aka the output of the fix sub-command. give her the goods and she'll do the rest 🍓

💜 options:

• -h, --help — shows this help message and then dips. classic. ✨
• -s SEGMENT, --segment SEGMENT — your segmentation calls file, the .cns one, which is the output of the segment command (yes with the extra ) in the original, she's quirky like that 🙈).
• -t THRESHOLD, --threshold THRESHOLD — the copy number change threshold you need to hit before a gene gets reported as a gain or a loss. [Default: 0.2] ⭐
• -m MIN_PROBES, --min-probes MIN_PROBES — the minimum number of covered probes required before she'll report a gain or loss. [Default: 3] 💅
• --drop-low-coverage — drops the very-low-coverage bins before segmentation, which is lowkey important because it avoids those false-positive deletions in poor-quality tumor samples. protective queen 🛡️
• -y, --male-reference, --haploid-x-reference — assumes the inputs were normalized to a male reference. so like, female samples will end up with +1 log-coverage on chrX; otherwise male samples would have -1 on chrX. pick your fighter 🧬
• -x {m,y,male,Male,f,x,female,Female}, --sample-sex {m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female} — specifies the sample's chromosomal sex as male or female. and if you don't tell her? she'll guess it from the X and Y coverage, which is honestly iconic of her 👑
• -o FILENAME, --output FILENAME — the output table file name. name your baby 💖

🌈 Statistics available:

• --mean — mean log2-ratio (unweighted).
• --median — median. the middle child, literally 😭
• --mode — mode, aka the peak density of log2 ratios.
• --ttest — a one-sample t-test of the bin log2 ratios versus 0.0.
• --stdev — standard deviation.
• --sem — standard error of the mean.
• --mad — median absolute deviation (standardized).
• --mse — mean squared error.
• --iqr — inter-quartile range.
• --bivar — Tukey's biweight midvariance. fancy fr fr 🔥
• --ci — confidence interval (by bootstrap).
• --pi — prediction interval.
• -a ALPHA, --alpha ALPHA — the level used to estimate confidence and prediction intervals. use it with --ci and --pi. [Default: 0.05]
• -b BOOTSTRAP, --bootstrap BOOTSTRAP — how many bootstrap iterations to run when estimating the confidence interval; use it with --ci. [Default: 100] 🎀

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ngl bestie, the defaults are doing a LOT of heavy lifting here — clock them before you go changing anything 💀

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and that's the whole page!! cnvkit.py genemetrics 0.9.10, born July 2023 🦋 she's a 0.9.10 girlie from July 2023 and she ate, no cap. mwah 💋 👑