GETGENEEXPRESSION(1)

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

💖 GETGENEEXPRESSION 💖

okay so real quick bestie — this is the manual for getGeneExpression, it lives in the User Commands section of the manual (section 1, iykyk), and it ships with getGeneExpression 0.7.5+dfsg from September 2021. I'm gonna walk you through the whole thing, no skips, no skimming, we're doing this properly 💅

✨ NAME ✨

getGeneExpression — compute expression of whole genes 🧬

🌸 SYNOPSIS 🌸

getGeneExpression -o <outFileName> -t <trInfoFileName>  [OPTIONS]
[samplesFile]

your girl needs at minimum an output file and a transcript info file. everything else is vibes 🦋

🎀 DESCRIPTION 🎀

So basically: it computes expression of whole genes. That's the whole thing. That's the assignment and it ate. 👑

  • [samplesFile] should contain transposed MCMC samples — which then get transformed into gene expression samples. It's giving glow-up, honestly. ✨

💅 OPTIONS 💅

one bullet per option, no gatekeeping, no skipping, here we go:

  • --help — shows you this help information. the classic. your friend when you're lost 🫶
  • -a, --adjustByLength — adjusts expression by transcripts length. (default: Off) 📏
  • -g <geneInfoFile>, --geneInfoFile=<geneInfoFile> — the name of the file to which the gene information will be saved. that's where the gene info goes bestie 🗂️
  • -G <geneListFile>, --geneList=<geneListFile> — the name of the file holding the list of gene names — one for each transcript, okay, one each, we're being precise here 🎀
  • -l, --log — outputs logged values. (default: Off) take the log of it, why not 🔥
  • -o <outFileName>, --outFile=<outFileName> — the name of the output file. yes you need it, it's literally in the SYNOPSIS 💖
  • --theta2rpkm — transforms transcript expression in theta to gene expression in RPKM. (default: Off) the transformation is real 🦋
  • -t <trInfoFileName>, --trInfoFile=<trInfoFileName> — the name of the transcript file. essential, iconic, required 💜
  • -T <trMapFile>, --trMap=<trMapFile> — the name of the file containing the transcript to gene mapping. the map that maps. the plot of the whole operation 🗺️
  • --updateTrFile — updates trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off) refresh her, give her new info 🌈
  • -v, --verbose — verbose output. (default: Off) she talks more. we love that 🙈
just a heads up bestie, defaults are defaults — if it says default: Off, it's off until you say otherwise. no assumptions, no cap 🫶

and that's the whole page!! every flag, every file, every default, all accounted for, nothing left behind 💜 go compute some gene expression, you got this, main character energy only ✨

— written by your bestie, getGeneExpression 0.7.5+dfsg, September 2021 — 🎀🦋💅

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