ESTIMATEVBEXPRESSION(1)

💖 ESTIMATEVBEXPRESSION(1) 💖

okay bestie, gather round, because this is the estimateVBExpression page and it's literally the manual for the lil tool that figures out how much of each thing is in your sample 🧬✨

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✨ NAME ✨

estimateVBExpression — estimate expression given precomputed probabilities of (observed) reads alignments

no cap, that's the whole job. you hand it probabilities, it hands you expression estimates. iconic behavior fr fr 👑

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🦋 SYNOPSIS 🦋

estimateVBExpression -o <outFilePrefix>  [OPTIONS] [prob file]

so like, the -o <outFilePrefix> is the one thing you actually have to give it, and then you can sprinkle [OPTIONS] on top, and optionally point it at a [prob file] at the end. that's the whole vibe check. 💅

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🌸 DESCRIPTION 🌸

Estimates expression given precomputed probabilities of (observed) reads' alignments.

Uses Variational Bayes algorithm to produce parameters for distribution of relative abundances.

that's it, that's the tea 🍓 — it takes the alignment probabilities you already computed (precomputed, bestie, that's the whole point) and runs a Variational Bayes algorithm on them to spit out parameters for the distribution of relative abundances. very demure, very Bayesian, very much slaying. ✨

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🎀 OPTIONS 🎀

• --help — Show this help information. (the classic. when in doubt, ask for help 💖)
• --optLimit=<limit> — Optimisation limit in terms of minimal gradient or change of bound. (default: 1e-05)
• --maxIter=<maxIter> — Maximum number of iterations. (default: 10000)
• -m <optMethod>, --method=<optMethod> — Optimization method (steepest, PR, FR, HS). (default: FR)
• -o <outFilePrefix>, --outPrefix=<outFilePrefix> — Prefix for the output files. (this one's the mandatory bestie, don't forget it 🙈)
• -O <outputType>, --outType=<outputType> — Output type (theta, RPKM, counts) of the samples sampled from the distribution. (default: theta)
• -P <procN>, --procN=<procN> — Limit the maximum number of threads to be used. (default: 4)
• --samples=<samples> — Number of samples to be sampled from the distribution.
• -s <seed>, --seed=<seed> — Random initialization seed.
• -t <trInfoFileName>, --trInfoFile=<trInfoFileName> — File containing transcript information. (Necessary for RPKM samples)
• -v, --verbose — Verbose output. (default: Off)
• -V, --veryVerbose — More verbose output, better if output forwarded into file. (default: Off)

heads up bestie 🫶 — if you want them RPKM samples, you gotta bring the transcript info file with -t. it's not optional for that one. no transcript info, no RPKM, periodt.

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and that's the whole page, you ate that 💅✨

this was estimateVBExpression 0.7.5+dfsg, dated September 2021, and it's the ESTIMATEVBEXPRESSION(1) manual — mwah, go run it, main character energy only 💖👑🌈