


  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 corre-
        sponding 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  inci-
        dent 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                          1


