.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
.TH "SAINT-SPC-CTRL" "1" "April 2012" "User Commands"
.SH NAME
saint-spc-ctrl \- run SAINT with control data
.SH SYNOPSIS
.B saint-spc-ctrl
.I [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [lowMode] [minFold] [normalize]
.SH DESCRIPTION
.IP
nburnin = 2000: number of burn\-in iterations in MCMC.
.IP
niter = 10000: number of main iterations in MCMC.
.IP
lowMode = 0/1 : exclude extremely high counts in the model.
.IP
\- If baits are densely connected or dataset is small (few baits), use 1.
.IP
\- otherwise, use 0.
.IP
minFold = 0/1 : forcing separation between true and false distributions.
.IP
\- If user wishes to allow typical contaminants with significant
.IP
differential enrichment over control purifications, use 0.
.IP
\- otherwise, use 1.
.IP
normalize = 0/1 : divide the counts by the total spectral counts in each IP.
.IP
nburnin = 2000: number of burn\-in iterations in MCMC.
.IP
niter = 10000: number of main iterations in MCMC.
.IP
lowMode = 0/1 : exclude extremely high counts in the model.
.IP
\- If baits are densely connected or dataset is small (few baits), use 1.
.IP
\- otherwise, use 0.
.IP
minFold = 0/1 : forcing separation between true and false distributions.
.IP
\- If user wishes to allow typical contaminants with significant
.IP
differential enrichment over control purifications, use 0.
.IP
\- otherwise, use 1.
.IP
normalize = 0/1 : divide the counts by the total spectral counts in each IP.
.SH "SEE ALSO"
You can download a PDF file with more detailed instructions from
.IP
http://sourceforge.net/projects/saint-apms/files/
.P
which is called saint-vignette-<YYYYMonDD>.pdf.