mcxalter.azm

\import{mcx.zmm}

\begin{pud::man}{

   {name}{mcxalter}
   {html_title}{The mcxalter manual}
   {author}{Stijn van Dongen}
   {section}{1}
   {synstyle}{long}
   {defstyle}{long}

   \man_share
}

\${html}{\"pud::man::maketoc"}

\sec{name}{NAME}
\NAME{mcxalter}{various network transformations}

\sec{synopsis}{SYNOPSIS}
\par{
   \mcxalter
   \synoptopt{-imx}{<fname>}{specify matrix/graph input}
   \synoptopt{-abc}{<fname>}{specify label input}
   \synoptopt{-tab}{<fname>}{use tab file}
   \synoptopt{-icl}{<fname>}{specify cluster input}
   \synoptopt{--block}{use within-cluster edges}
   \synoptopt{--blockc}{use between-cluster edges}
   \synoptopt{-o}{<fname>}{output}
   \shared_synoptopt{-tf}

   }

\sec{description}{DESCRIPTION}

\par{
   This utility supplies various transformations of networks.

   }


\sec{options}{OPTIONS}

\begin{itemize}{\mcx_itemopts}

\item{\defopt{-abc}{<fname>}{label input}}
\car{
   The file name for input that is in label format.}

\item{\defopt{-imx}{<fname>}{input matrix}}
\car{
   The file name for input that is in mcl native matrix format.}

\item{\defopt{-tab}{<fname>}{use tab file}}
\car{
   This option causes the output to be printed with the labels
   found in the tab file.
   With \genopt{-abc} this option will, additionally, construct
   a graph only on the labels found in the tab file.
   If this option is used in conjunction with \genopt{-imx} the
   tab domain and the matrix domain are required to be identical.
   }


\item{\defopt{-icl}{<fname>}{specify cluster input}}
\car{
   Read in a cluster file for use with either \genopt{--block} or \genopt{--blockc}.
   }

\item{\defopt{--block}{use within-cluster edges}}
\car{
   Remove between-cluster edges from the network. This is done first, before
   other transformations take effect.
   }

\item{\defopt{--blockc}{use between-cluster edges}}
\car{
   Remove within-cluster edges from the network. This is done first, before
   other transformations take effect.
   }


\shared_itemopt{-tf}
\car{\shared_defopt{-tf}}

\item{\defopt{-o}{fname}{output file}}
\car{
   Output file.}

\end{itemize}


\sec{author}{AUTHOR}
\par{
   Stijn van Dongen.
   }

\sec{seealso}{SEE ALSO}
\par{
   \mysib{mcxio},
   \mysib{mcx},
   \mysib{mcxsubs},
   and \mysib{mclfamily} for an overview of all the documentation
   and the utilities in the mcl family.
   }

\end{pud::man}