RSEM-CONTROL-FDR(1)

📦
version 1.3.3 · 5 versions
, in ubuntu noble, ubuntu resolute

✨ RSEM-CONTROL-FDR ✨

okay bestie, pull up a chair 🎀 this is the rsem-control-fdr page from your friendly neighborhood User Contributed Perl Documentation, and it's literally just vibes + math. lowkey it's the bouncer at the club that checks your genes' IDs before letting them in the DE list 💅

🌸 NAME 🌸

rsem-control-fdr — filter EBSeq output for statistical significance. no cap, that's the whole job. it takes the big messy results and keeps only the ones that passed the vibe check 🦋

✨ SYNOPSIS ✨

rsem-control-fdr [options] input_file fdr_rate output_file

three positional args, options optional, and honestly? that's it. iconic.

🧚 ARGUMENTS 🧚

  • input_file — this one HAS to be the main result file that rsem-run-ebseq made for you. it's the one holding every gene and transcript together with all their associated statistics. the whole roster, fr fr.
  • fdr_rate — the desired false discovery rate (FDR). yes, the actual FDR you want. you type it, we honor it. ✨
  • output_file — this file is a subset of the input_file. it only contains the genes/transcripts that got called as differentially expressed (DE). 🎉
okay so when more than 2 conditions exist, DE is defined as not all conditions are equally expressed. that's the definition, periodt.

and like, huge reminder: statistical significance does NOT necessarily mean biological significance 😭 so please, also refer to the fold changes to decide which genes/transcripts are actually biologically significant. stats said yes, biology might say "ma'am this is nothing."

also — when more than two conditions exist, this file will not contain fold change information and you'll have to calculate it from input_file.condmeans by yourself. sorry bestie, you're on your own for that one 🙈

💅 OPTIONS 💅

  • --hard-threshold — use the hard threshold method to control FDR. if you set this, only those genes/transcripts with their PPDE >= 1 - fdr_rate get called as DE. strict queen behavior. (Default: on) 👑
  • --soft-threshold — use the soft threshold method to control FDR. if you set this, the program will try to report as many genes/transcripts as possible, as long as their average PPDE >= 1 - fdr_rate. this option is equivalent to using EBSeq's crit_fun for FDR control. generous queen behavior, she wants everybody in the group chat. (Default: off) 🫶
  • -h/--help — show help information. when in doubt, ask. 💖

🌈 DESCRIPTION 🌈

this program controls the false discovery rate and reports differentially expressed genes/transcripts. that's the mission statement, and she ate. 🔥

🍓 EXAMPLES 🍓

say we've got GeneMat.results as our input (we do, trust). we want to control FDR at 0.05 using the hard threshold method, and we want the output file named GeneMat.de.txt:

rsem-control-fdr GeneMat.results 0.05 GeneMat.de.txt

boom. done. go forth and interpret responsibly 🧚✨

reminder that the hard threshold method is the default one, so if you just run the command above with no flags, you already get it. no extra typing required, we love efficiency 💜

and that's the whole page bestie!! 🎀 this was perl v5.38.2, dated 2024-04-14 — from me to you, mwah 💋 stay significant, but not too significant, iykyk 🌸🦋

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