saint-spc-ctrl - run SAINT with control data
saint-spc-ctrl [interactionFile] [preyFile] [baitFile]
[nburnin] [niter] [lowMode] [minFold] [normalize]
- 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.
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.