mcxalter(1)                     USER COMMANDS                      mcxalter(1)



  NAME
      mcxalter - various network transformations

  SYNOPSIS
      mcxalter [-imx <fname> (specify matrix input)] [-abc <fname> (specify
      label input)] [-tab <fname> (use tab file)] [-o <fname> (output)]
      [-ceil-nb n (reduce neighbourhoods)] [-knn-mutual n (keep mutually close
      neighbours)] [-tf spec (apply tf-spec to input matrix)]

  DESCRIPTION
      This utility supplies various transformations of networks.

  OPTIONS
      -abc <fname> (label input)
        The file name for input that is in label format.

      -imx <fname> (input matrix)
        The file name for input that is in mcl native matrix format.

      -tab <fname> (use tab file)
        This option causes the output to be printed with the labels found in
        the tab file.  With -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 -imx the tab domain and the matrix domain are
        required to be identical.

      -tf <tf-spec> (transform input matrix values)
        Transform the input matrix values according to the syntax described in
        mcxio(5).

      -ceil-nb n (reduce neighbourhoods)
        The nodes of the input graph are considered in descending order of the
        number of neighbours they posses. The first nodes has it neighbours of
        lowest edge weight removed until no more than N remain. The
        corresponding reciprocal edges from nodes further down the list are
        removed as well. Subsequent nodes are treated in the same way until
        all nodes in the graph have at most N neighbours. This may be
        considered a poor man's hub removal.

      -knn-mutual <num> (keep mutually close neighbours)
        This considers the <num> best neighbours for each node, then only
        keeps edges that occur in both best-neighbour lists for the two
        incident nodes.

      -o fname (output file)
        Output file.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all
      the documentation and the utilities in the mcl family.



  mcxalter 1.008, 09-308            4 Nov 2009                       mcxalter(1)
