mcxalter(1)                     USER COMMANDS                      mcxalter(1)



  NAME
      mcxalter - various network transformations

  SYNOPSIS
      mcxalter [-imx <fname> (specify matrix/graph input)] [-abc <fname>
      (specify label input)] [-tab <fname> (use tab file)] [-icl <fname>
      (specify cluster input)] [--block (use within-cluster edges)] [--blockc
      (use between-cluster edges)] [-o <fname> (output)] [-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.

      -icl <fname> (specify cluster input)
        Read in a cluster file for use with either --block or --blockc.

      --block (use within-cluster edges)
        Remove between-cluster edges from the network. This is done first,
        before other transformations take effect.

      --blockc (use between-cluster edges)
        Remove within-cluster edges from the network. This is done first,
        before other transformations take effect.

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

      -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 14-137                   16 May 2014                      mcxalter(1)
