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\def{"man::synstyle"}{long}
\def{"man::defstyle"}{long}
\import{mcx.zmm}
\set{"man::name"}{mcxarray}
\set{"man::html-title"}{The mcxarray manual}
\set{"man::author"}{Stijn van Dongen}
\set{"man::section"}{1}
\"man::preamble"
\${html}{\"man::maketoc"}
\sec{name}{NAME}
\NAME{mcxarray}{Transform array data to MCL matrices}
\sec{synopsis}{SYNOPSIS}
\par
\mcxarray [options] <array data matrix>
\par
\mcxarray
\synoptopt{-o}{fname}{output file fname}
\synoptopt{-co}{num}{cutoff for output values}
\synoptopt{-gq}{num}{ignore input smaller than}
\synoptopt{-lq}{num}{ignore input larger than}
\synoptopt{-t}{work with the transpose}
\synoptopt{-ctr}{num}{add center (for graph-type input)}
\synoptopt{--ctr}{add center with default value (for graph-type input)}
\synoptopt{--01}{remap output to [0,1] interval}
\synoptopt{--cosine}{use cosine}
\synoptopt{--pearson}{use Pearson correlation (default)}
\synoptopt{-tear}{num}{inflate input columns}
\synoptopt{-teartp}{num}{inflate tranposed columns}
\synoptopt{-pi}{num}{inflate the result}
<fname> (\it{array data matrix})
\sec{description}{DESCRIPTION}
\mcxarray reads a data file satisfying the mcl input format
(refer to \sibmcxio). By default it will work with the
columns as the data vectors (note that mcl matrices are
presented as a listing of columns). This can be changed using
the \optref{-t}{\genopt{-t} option}.
\sec{options}{OPTIONS}
\begin{itemize}
\item{\defopt{-o}{fname}{output file fname}}
Indeed.
\item{\defopt{-co}{num}{cutoff for output values}}
Output values smaller than \genarg{num} are removed (set to zero).
\item{\defopt{-gq}{num}{ignore input smaller than}}
Input values smaller than \genarg{num} are ignored.
\item{\defopt{-lq}{num}{ignore input larger than}}
Input values larger than \genarg{num} are ignored.
\item{\defopt{-t}{work with the transpose}}
Work with the transpose of the input data matrix.
\item{\defopt{-ctr}{num}{add center (for graph-type input)}}
Add diagonal values to the output according to a (so called)
\it{center} formula.
\item{\defopt{--ctr}{add center with default value (for graph-type input)}}
Same as \useopt{-ctr}{1.0}.
\item{\defopt{--01}{remap output to [0,1] interval}}
Rescale output values so that they are within the [0,1] interval.
\item{\defopt{--cosine}{use cosine}}
Use the cosine as correlation measure.
\item{\defopt{--pearson}{use Pearson correlation (default)}}
Compute the Pearson correleation coefficient as the
similarity between the data columns.
\item{\defopt{-tear}{num}{inflate input columns}}
Apply (column-wise) inflation with parameter \genarg{num} to the input
values before further processing.
\item{\defopt{-teartp}{num}{inflate tranposed columns}}
Apply (column-wise) inflation with parameter \genarg{num} to the input
values in the transposed matrix before further processing.
\item{\defopt{-pi}{num}{inflate the result}}
Apply inflation with parameter \genarg{num} to the output values.
\end{itemize}
\sec{author}{AUTHOR}
\par
Stijn van Dongen.
\sec{seealso}{SEE ALSO}
\sib{mcl},
\sib{mclfaq},
and \sibmclfamily for an overview of all the documentation
and the utilities in the mcl family.
\"man::postamble"
|
