SAINT-SPC-CTRL(1)

🎀 NAME 🎀

saint-spc-ctrl — run SAINT with control data

💅 SYNOPSIS 💅

saint-spc-ctrl [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [lowMode] [minFold] [normalize]

✨ DESCRIPTION ✨

okay so bestie, this is the control-data era of SAINT, and these are the knobs you get to turn. here's the whole lineup, no gatekeeping 🫶

• nburnin = 2000 — the number of burn-in iterations in MCMC. that's the lil warm-up arc before the real plot kicks in ✨
• niter = 10000 — the number of main iterations in MCMC. this is the main character part 💅
• lowMode = 0/1 — exclude extremely high counts in the model.
  • if baits are densely connected or the dataset is small (few baits), use 1.
  • otherwise, use 0.
• minFold = 0/1 — forcing separation between true and false distributions.
  • if the user wishes to allow typical contaminants with significant
  • differential enrichment over control purifications, use 0.
  • otherwise, use 1.
• normalize = 0/1 — divide the counts by the total spectral counts in each IP.

and then… yeah. it's literally all of that again, because the original page said it twice and we do not erase history in this house 😭💀

• nburnin = 2000 — number of burn-in iterations in MCMC.
• niter = 10000 — number of main iterations in MCMC.
• lowMode = 0/1 — exclude extremely high counts in the model.
  • if baits are densely connected or dataset is small (few baits), use 1.
  • otherwise, use 0.
• minFold = 0/1 — forcing separation between true and false distributions.
  • if user wishes to allow typical contaminants with significant
  • differential enrichment over control purifications, use 0.
  • otherwise, use 1.
• normalize = 0/1 — divide the counts by the total spectral counts in each IP.

🌈 SEE ALSO 🌈

you can download a PDF file with more detailed instructions from

http://sourceforge.net/projects/saint-apms/files/

which is called saint-vignette-<YYYYMonDD>.pdf. yes the filename literally has the date in it, iykyk 📄✨

and that's the whole vibe check, bestie 💖 it came out of the User Commands corner of the manual, dated April 2012, under the very iconic name SAINT-SPC-CTRL(1). go forth and slay those control purifications, no cap 👑🌸