ESTIMATEEXPRESSION(1)

📦
version 0.7.5 · 4 versions
, in ubuntu jammy, ubuntu noble

💅 ESTIMATEEXPRESSION — section 1 of the manuals, bestie

okay so this is the page for estimateExpression, a User Commands joint, and it's literally the whole vibe of "tell me how much of each transcript is actually there." sit down, grab a strawberry 🍓, we're doing this.

✨ NAME ✨

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

like. the probabilities are already done. we're just doing the vibes math on top. slay.

🦋 SYNOPSIS 🦋

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

yes the flag comes first, -o is not optional, she's the main character, she ate 👑

🌸 DESCRIPTION 🌸

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

Uses MCMC sampling algorithm to produce relative abundance or RPKM. no cap, that's the whole thing. MCMC walk in, relative abundance or RPKM walk out. it's giving statistical girlboss energy 🔥

🎀 OPTIONS 🎀

here's where it gets juicy. every single one, no skipping, we don't do that here 💖

  • --help — Show this help information. the classic "wait what does this do again" button 🙈
  • --MCMC_burnIn=<MCMC_burnIn> — Length of sampler's burn in period. (default: 1000)
  • --MCMC_chainsN=<MCMC_chainsN> — Number of parallel chains used. At least two chains will be used. (default: 4) — yes, at least two, she refuses to run solo, it's a group chat not a monologue 💅
  • --MCMC_dirAlpha=<MCMC_dirAlpha> — Alpha parameter for the Dirichlet distribution. (default: 1)
  • --MCMC_samplesDOmax — Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)
  • --MCMC_samplesN=<MCMC_samplesN> — Initial number of samples produced. Doubles after every iteration. (default: 1000) — she literally doubles every iteration, we love a growth mindset ✨
  • --MCMC_samplesNmax=<MCMC_samplesNmax> — Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)
  • --MCMC_samplesSave=<MCMC_samplesSave> — Number of samples recorder in total. (default: 1000) — (yes it says "recorder" in the original, we're leaving that exactly as-is, i don't make the rules 😭)
  • --MCMC_scaleReduction=<MCMC_scaleReduction> — Target scale reduction, sampler finishes after this value is met. (default: 1.2)
  • -G , --gibbs — Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)
  • -o <outFilePrefix> , --outPrefix=<outFilePrefix> — Prefix for the output files. this is the required one btw, don't forget her 🫶
  • -O <outputType> , --outType=<outputType> — Output type (theta, RPKM, counts, tau). (default: theta)
  • -p <parFileName> , --parFile=<parFileName> — File containing parameters for the sampler, which can be otherwise specified by --MCMC* options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running. — live editing your sampler mid-run?? the way that she checks the file every iteration, that's iconic behavior 🌈
  • -P <procN> , --procN=<procN> — Limit the maximum number of threads to be used. (Default is the number of MCMC chains.) — default is whatever --MCMC_chainsN said, keep up babes 👑
  • --scaleReduction — Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)
  • -s <seed> , --seed=<seed> — Random initialization seed. gotta have reproducible randomness, it's a whole thing ⭐
  • --thetaActFile=<thetaActFileName> — File for logging noise parameter theta^{act}.
  • -t <trInfoFileName> , --trInfoFile=<trInfoFileName> — File containing transcript information. (Necessary for RPKM) — NECESSARY for RPKM okay so if you want RPKM and you skip this, that's on you bestie 😭
  • -v , --verbose — Verbose output. (default: Off) — turn her on and she will Not stop talking. relatable 💀
friendly reminder from your local unix girlie: booleans like --gibbs, --scaleReduction, --MCMC_samplesDOmax and --verbose default to Off, and the ones with <angleBracket> placeholders want a value. and -o <outFilePrefix> is just... required. periodt 💜

that's the whole page, angel. this was estimateExpression version 0.7.5+dfsg, dated September 2021, living in manual section 1, and honestly? she's a little old but she's still serving. go estimate some expression, you've got this 💖✨🦋

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