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mcxalter(1) [debian man page]

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)] [-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).

      -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 12-068						      8 Mar 2012							 mcxalter(1)

Check Out this Related Man Page

clm close(1)							  USER COMMANDS 						      clm close(1)

  NAME
      clm close - Fetch connected components from graphs or subgraphs

      clmclose	is  not  in  actual  fact  a program. This manual page documents the behaviour and options of the clm program when invoked in mode
      close. The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.

  SYNOPSIS
      clm close -imx <fname> [options]

      clm close -imx fname (specify matrix input) -abc fname (specify label input) -dom fname (input domain/cluster file) [-o fname (output file)]
      [--is-undirected	(trust	input  graph  to  be  undirected)] [--write-count (output component count)] [--write-sizes (output component sizes
      (default))] [--write-cc (output components as clustering)] [--write-block (output graph restricted to -dom argument)] [--write-blockc  (out-
      put  graph  complement  of  -dom	argument)]  [-cc-bound	num  (select components with size at least num)] [-tf spec (apply tf-spec to input
      matrix)] [-h (print synopsis, exit)] [--apropos (print synopsis, exit)] [--version (print version, exit)]

  DESCRIPTION
      Use clm close to fetch the connected components from a graph. Different output modes are supported (see below). In matrix mode  (i.e.  using
      the  -imx option) the output returned with --write-cc can be used in conjunction with mcxsubs to retrieve individual subgraphs corresponding
      to connected components.

  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.

      -o fname (output file)
	Specify the file where output is sent to. The default is STDOUT.

      -dom fname (input domain/cluster file)
	If this option is used, clm close will, as a first step, for each of the domains in file fname retrieve the associated subgraph  from  the
	input graph. These are then further decomposed into connected components, and the program will process these in the normal manner.

      --write-count (output component count)
      --write-sizes (output component sizes (default))
      --write-cc (output components as clustering)
      --write-block (output graph restricted to -dom argument)
      --write-blockc (output graph complement of -dom argument)
	The  default  behaviour  is  currently to output the sizes of the connected components. It is also possible to simply output the number of
	components with --write-count or to write the components as a clustering in mcl format with -write-cc. Even more options exist: it is pos-
	sible to output the restriction of the input graph to a domain, or to output the complement of this restriction.

      --is-undirected (omit graph undirected check)
	With  this option the transformation to make sure that the input is undirected is omitted. This will be slightly faster. Using this option
	while the input is directed may lead to erronenous results.

      -cc-bound num (select components with size at least num)
	Transform the input matrix values according to the syntax described in mcxio(5).

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  clm close 12-068						      8 Mar 2012							clm close(1)
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