## 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.