SAINT-SPC-NOCTRL(1)

✨ SAINT-SPC-NOCTRL ✨

okay bestie, welcome to the saint-spc-noctrl page from the User Commands corner of the manual, no cap 💅

🎀 NAME 🎀

saint-spc-noctrl — run the SAINT scoring algorithm for protein-protein interaction data, using label free quantitative proteomics data 🧚

🌸 SYNOPSIS 🌸

saint-spc-noctrl [interactionFile] [preyFile] [baitFile] [nburnin]
[niter] [fthres] [fgroup] [var] [normalize]

💖 DESCRIPTION 💖

okay so here's the tea, the flags are literally all positional arguments and they go in this order, periodt:

• -burnin and iter — this is the burn-in period and the main iteration of the MCMC. yes, the MCMC. she's doing Markov chain Monte Carlo, main character energy fr fr 🔥
• -fthres — the frequency threshold. above this threshold the probability gets set to 0. it's giving "we're cutting you off at this line" 💀
• -fgroup — the frequency boundary that divides the high frequency group from the low frequency group. two friend groups, one boundary, iykyk ✨
• -var — a binary [0/1] indicator for modeling the variance of the count data distributions. just 0 or 1 bestie, no in-between 🦋
• -normalize — whether to normalize the counts by total spectral counts. yes or no, that's the whole vibe check 🌈

👑 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. go read her, she ate 💜

so that's the whole page!! this was saint-spc-noctrl, part of the SAINT crew, dated April 2012 🌸 thank you for coming to my ted talk, ily, mwah 🫶💖⭐