saint-spc-noctrl(1) [debian man page]

SAINT-SPC-NOCTRL(1)						   User Commands					       SAINT-SPC-NOCTRL(1)

NAME

       saint-spc-noctrl - run SAINT scoring algorithm for protein-protein interaction data using label free quantitative proteomics data

SYNOPSIS

       saint-spc-noctrl [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [fthres] [fgroup] [var] [normalize]

DESCRIPTION

       -burnin and iter: burn-in period and main iteration of MCMC

       -fthres: frequency threshold above which probability is set to 0

       -fgroup: frequency boundary dividing high and low frequency groups

       -var: binary [0/1] indicator for modeling variance of the count data distributions

       -normalize: whether to normalize the counts by total spectral counts

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.

saint-spc-noctrl						    April 2012						       SAINT-SPC-NOCTRL(1)

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)