SAINT-SPC-CTRL(1) General Commands Manual SAINT-SPC-CTRL(1)
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.
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.
User Commands April 2012 SAINT-SPC-CTRL(1)
