debian man page for saint-spc-ctrl

Query: saint-spc-ctrl

OS: debian

Section: 1

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

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)
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