


  mcx q(1)                  USER COMMANDS                  mcx q(1)


  NAME
      mcxquery - compute simple graph statistics

  SYNOPSIS
      mcxq  is  not  in  actual fact a program. This manual page documents the
      behaviour and options of the mcx program when invoked  in  mode  q.  The
      options  -h,  --apropos,  --version,  -set,  --nop,  -progress <num> are
      accessible in all mcx modes. They are described in the mcx manual  page.

      mcxquery  [-imx <fname> (specify matrix input)] [-o <fname> (output file
      name)] [-vary-threshold <start,end,step,scale> (analyze graphs at  simi-
      larity cutoffs)] [--vary-correlation (analyze graphs at correlation cut-
      offs)] [-div <num> (cluster size separating value)] [-report-scale <num>
      (edge weight/threshold scaling)] [--dim (report native format and dimen-
      sions)] [-h (print synopsis, exit)] [--apropos (print  synopsis,  exit)]
      [--version (print version, exit)]

  DESCRIPTION
      The  main  use of mcxquery is to analyze a graph at different similarity
      cutoffs. Typically this is done on a graph constructed using a very per-
      missive  threshold.  For  example,  one  can  create  a graph from array
      expression data using mcxarray with a very low pearson correlation  cut-
      off  such  as 0.2 or 0.3. Then mcxquery can be used to analyze the graph
      at  increasingly  stringent  thresholds  of 0.25,  0.30,   0.35 .. 0.95.
      Attributes  supplied  across different thresholds are the number of con-
      nected components, statistics (median, average, iqr) on node degrees and
      edge  weights, and a graph plotting the R^2 value of the relationship of
      log(k) versus the logarithm of the number of nodes of degree at least  k
      (for  the  graph at a given threshold).  Scale-free networks are defined
      by having a high R^2 value. It should be  noted  however  that  in  many
      applications  graphs will not be scale-free.  Additionally, for the pur-
      pose of clustering scale-free networks are to be avoided or transformed,
      as  the  highly-connected nodes in scale-free networks obfuscate cluster
      structure.

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

      -o <fname> (output file name)
        Set the name of the file where output should be written to.

      --dim (report native format and dimensions)
        This will report the matrix format (either interchange or binary)  and
        the  matrix dimensions. For a graph the two reported dimensions should
        be equal.

      -vary-threshold <start,end,step,scale> (analyze graphs at similarity cutoffs)
        All of start, end, step and scale must be integer numbers. From  these
        a  list  of  threshold  is  constructed,  starting from start / scale,
        (start + step) / scale, (start + 2 step) / scale, and so  on  until  a
        value larger than or equal to end / scale is reached.

      --vary-correlation (analyze graphs at correlation cutoffs)



  mcx q 1.008, 09-308         4 Nov 2009                          1





  mcx q(1)                  USER COMMANDS                  mcx q(1)


        This  instructs mcxquery to use a threshold list suitable for use with
        graphs in which the edge weight  similarities  are  correlation.   The
        list  start  at  0.2  and ends at 0.95, with increments of 0.05.  If a
        different start or increment is required it can be achieved  by  using
        the  -vary-threshold  option.   For  example,  a  start of 0.10 and an
        increment      of 0.02      are       obtained       by       issueing
        -vary-threshold 10,100,2,100.

      -report-scale <num> (edge weight / threshold scaling)
        The  edge  weights mean, average, and inter-quartile range, as well as
        the different threshold steps are all rescaled in the reported  output
        to avoid printing of fractional part.  If -vary-threshold was supplied
        then scaling factor specified in the argument is used.   With  --vary-
        correlation  a scaling factor of 100 is used. Either can be overridden
        by using the present option.

      -div <num> (cluster size separating value)
        When analyzing graphs at different thresholds with one of the  options
        above,  mcxquery reports the percentage of nodes contained in clusters
        not exceeding a specified size, by  default 3.   This  number  can  be
        changed using the -div option.

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
































  mcx q 1.008, 09-308         4 Nov 2009                          2


