CONVERTSAMPLES(1)

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

👑 CONVERTSAMPLES — the convertSamples manual, but make it cute

okay bestie, gather round, because tonight we're talking about convertSamples — the little program that converts or normalizes your MCMC expression samples. yes, that MCMC. the Markov Chain Monte Carlo one. she's niche, she's powerful, she ate 💅

🌸 NAME 🌸

convertSamples — convert or normalize MCMC expression samples. that's literally her whole job. no cap. ✨

🎀 SYNOPSIS 🎀

convertSamples -a <action> -o <outFileName>  [OPTIONS] [sampleFile]

like... two flags are required, bestie. -a and -o. the rest is choose-your-own-adventure 🦋

💖 DESCRIPTION 💖

So basically: convertSamples converts or normalizes MCMC expression samples. iconic behavior honestly.

and just so we're clear on the vibes, listen up:

  • [sampleFile] should contain transposed MCMC samples. transposed!! not regular!! if your samples aren't transposed you're gonna have a bad time, and not in the cute way. 😭

✨ OPTIONS ✨

  • --help — shows this help information. short, sweet, helpful. a lil angel 🫶
  • --Nmap=<Nmap> — the total number of aligned reads. OR, when you're normalizing, it's your normalization constant. dual purpose queen 👑
  • -a <action>, --action=<action> — the action to perform. here are the options, and there are a LOT of them, so let's go one by one:
    • T2R — theta to rpkm 💫
    • R2T — rpkm to theta 💫
    • T2RL — theta to log-rpkm 💫
    • C2R — counts to rpkm 💫
    • R2C — rpkm 2 counts 💫
    • NORM — normalize. (samples are multiplied by Nmap) 🧚
    • LOGNORM — log+normalize. (samples are multiplied by Nmap and logged) 🔥
  • -o <outFileName>, --outFile=<outFileName> — the name of the output file. tell her where to write it, she's not a mind reader 💀
  • -t <trInfoFileName>, --trInfoFile=<trInfoFileName> — the file containing transcript information. give her the transcript lore 📜
  • -v, --verbose — verbose output. default: Off. turn it on if you want her to talk to you more, which honestly, same ✨
tiny reminder bestie: -a and -o are not optional, they're the whole point. everything else is seasoning 🌈

🦋 a lil farewell 🦋

that's the whole page, mwah. this little doc is from convertSamples 0.7.5+dfsg, dated September 2021 — so she's been serving conversion and normalization since way back, and she still eats every time. stan. 🎀💜

now go transpose your samples first, i'm serious, bestie. bye!! 👋🌸

📦 where this page comes from