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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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