GETPPLR(1)

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

🌸 getPPLR(1) — the manual page, but make it a group chat 🌸

okay bestie, welcome to getPPLR, from section 1 of the manual (that's User Commands, aka "stuff you just type, no root required 💅"). This is genuinely one of those tools that sounds scary and is actually just doing math on your behalf while you sip your lil drink. Let's get into it.

✨ NAME ✨

getPPLR — compute PPLR from MCMC expression samples 💖

That's it, that's the whole job. PPLR. From MCMC. From your expression samples. Iconic behavior, honestly.

🦋 SYNOPSIS 🦋

getPPLR -o <outFileName>  [OPTIONS] [sampleFile-C1] [sampleFile-C1]

so yeah, you need -o <outFileName> (she's required, she's the main character 👑) and then whatever else you want after that. Note that the sample file placeholders are literally written as [sampleFile-C1] [sampleFile-C1] — yes, twice, same name, that's what the page says, and I'm not about to start editing the sacred texts. It's giving "two conditions, put your files in order" vibes. 🫶

🌈 DESCRIPTION 🌈

Computes PPLR from MCMC expression samples. 🧬✨

(the probability of second condition being up-regulated)

and it also computes log2 fold change with confidence intervals, plus the condition mean log expression. So like, three little treats in one command. Obsessed.

The [sampleFiles] should contain transposed MCMC samples from different conditions. Transposed, bestie. Do not come in here with untransposed samples, it's not the vibe. 🙈

💜 OPTIONS 💜

  • --help — show this help information. The "hello, what does anything do" button. You love to see it. 🎀
  • -d, --distribution — produce the whole distribution of differences. Not just the summary, the entire spread. default: Off ✨
  • --inputIsLogged — tells the tool your input expression estimates are on a log scale. Also: you do not need to use this with data generated by BitSeq-0.5.0 and above, so if that's you, chill. (default: Off) 🌸
  • -o <outFileName>, --outFile=<outFileName> — name of the output file. This one's mandatory, no skipping, she's the whole point. 💅
  • -s <selectFileName>, --selectFile=<selectFileName> — a file containing a list of selected transcript IDs (zero based), and only those get reported. Heads up though: this only works with the --distribution option. So it's a package deal, don't try to run it solo. 🦋
  • --subSample=<subSample> — sub-sample the distributions using a given fraction of expression samples. (default: 1) 🍓
  • -v, --verbose — verbose output. She talks more. (default: Off) 🔥

👑 a lil sign-off 👑

This whole thing is from getPPLR 0.7.5+dfsg, dated September 2021 — so if you're out here in the future wondering why something looks a lil retro, that's why, and she's still serving 💖 no cap. Now go run your samples, bestie, and remember: transposed, -o always, -s only with -d. periodt. 🌟

📦 where this page comes from