This is the command saint-spc-ctrl that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
saint-spc-ctrl - run SAINT with control data
SYNOPSIS
saint-spc-ctrl [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [lowMode]
[minFold] [normalize]
DESCRIPTION
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.
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.
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