saint-spc-ctrl(1) [debian man page]
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)
Check Out this Related Man Page
MAPHIMBU(1) User Commands MAPHIMBU(1) NAME
maphimbu - histogram builder for 1-d numerical and text data SYNOPSIS
maphimbu [OPTION]... [FILE] DESCRIPTION
This program produces 1-d histograms from numerical or text data input. It can be also used to estimate the probability distribution func- tion of a numerical variable - see http://en.wikipedia.org/wiki/Probability_density_function. OPTIONS
-x <int> x-data column (default is 1) -y <int> y-data column (default is 2); It is considered only when combined with '-m' or '-S' -d <float|int> delta size (dx-resolution) in case of numerical data; Keep in mind that 2 is not the same as 2.0: in the first case the numbers are treated as integers, in the latter as floats. -n normalize the result A) non-numerical data: n(x) = counts(x)/sum_of_counts B) numerical data: the normalized probability density func. is P(-INF < x <INF) = Int_[-INF:INF] P(x)*dx = 1 ; For the numerical integration an open x-data interval is assumed. -N normalize data against the total sum of counts (same as option '-n' with case A forced) -U normalize the result with x-range mapped to unit; The x-values are mapped to the interval [0:1], respectively Int_[0:1] P(x)*dx = 1; This option is mutually exclusive with '-n'. -S compute sums and normalized sums of y-values; The total sum of all y-values is used for the normalization. -m compute the arithmetic mean of y-values in the respective x-bar -s <int> sort output using the specified column; Header is skipped in this case. -g <int> sort output numerically using the specified column; Header is skipped in this case. -r do reverse sorting (in combination with '-g' and '-s') -C center histogram bars (shifts x-axis by 0.5*dx) -X treat hole line as one string (single data record) -H print a data description header -V print program version and exit --version output version and copyright information --help display help -h display short help (options summary) Note: this program is not intended for use in high order numerical computations. REPORTING BUGS
Report bugs to <gnu@mirendom.net> COPYRIGHT
Copyright (C) 2003-2007, 2009, 2011 Dimitar Ivanov License: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. maphimbu 2.8.4 February 2012 MAPHIMBU(1)