ProbABEL(1)

💖 ProbABEL(1) 💖

okay so bestie, welcome to the General Commands Manual glow-up of ProbABEL — this is the page for the probabel command, and honestly? it's giving convenience. let's get into it 🫶

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✨ NAME ✨

probabel — a wrapper around the three ProbABEL binaries, here to make your life so much easier 💅

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✨ SYNOPSIS ✨

probabel CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE
[OTHER_OPTIONS]

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✨ DESCRIPTION ✨

so probabel is literally a wrapper around the three ProbABEL binaries, and those are:

• palinear
• palogist
• pacoxph

she exists to make running a Genome-Wide Association Study (GWAS) way less of a whole thing, and she saves your precious time in two ways, no cap:

1. she runs the regression analysis of all the chromosomes from CHROM-START to CHROM-STOP, back to back, no manual babysitting required 🌈
2. unlike those three binaries up there, with probabel you do not have to specify where all the required genetic data files live. their location is centrally managed in a configuration file, and that file is /etc/probabel_config.cfg by default. iconic behavior honestly 👑

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✨ OPTIONS ✨

🌸 Required command line options 🌸

• CHROM-START — the number of the chromosome to start the analysis at. the beginning of the journey, if you will 🦋
• CHROM-END — the number of the chromosome to end the analysis at. the finish line bestie 🎀

fr fr: you can run a single chromosome all by itself by putting the same number for CHROM-START and CHROM-STOP. and that's actually the way to run the analysis for the X or Y chromosome, so don't sleep on it 💀

• METHOD — which regression method to use. it can be one of linear, logistic, or coxph. pick your fighter ⭐
• COHORT — the name of the cohort as it's defined in the /etc/probabel_config.cfg file. using that cohort identifier from the config file, the three actual ProbABEL binaries know where to find the genotypic information files (that's the dosage files and/or probability files) 👀
• MODEL — the genetic model to be used. can be either --additive for the additive model (which requires genotype data in dosage form), or --allmodels to run all the genetic models: additive, recessive, dominant, over-dominant and 2df. she does the whole lineup 💅
• PHENOTYPE — the name of the phenotype file, without its extension (and that extension should be .PHE!) 🍓

🌈 Other options 🌈

any options you list after the (mandatory) ones up there get passed on to the underlying binary — so palinear, palogist or pacoxph, depending on the METHOD. it's a handoff, she's just the messenger 🧚

the most commonly used option is the -o option, followed by a file name. this specifies the beginning of the file name for the output files. lowkey the one you'll reach for constantly ✨

💜 Additional options 💜

• -h, --help — get additional help on how to run probabel. and the best part? in this case none of the other options need to be specified. a stress-free experience, we love to see it 😭

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✨ EXAMPLES ✨

this one runs a genome-wide association scan using linear regression and the additive genetic model on cohort My_Large_Cohort for phenotype my_phenotype:

probabel 1 22 linear "My_Large_Cohort" --additive my_phenotype

ate. no crumbs. 🔥

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✨ SEE ALSO ✨

palinear(1), palogist(1), pacoxph(1)

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✨ BUGS ✨

found a bug? the bugtracker is located at:

https://github.com/GenABEL-Project/ProbABEL/issues

go tell them, bestie, they wanna know 🙈

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✨ AUTHORS ✨

Lennart C. Karssen 👑

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and that's the whole page! this was ProbABEL 0.5.0, dated 4 May 2016, from the ProbABEL(1) manual — ty for reading, mwah 💖