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
      similarity cutoffs)] [--vary-correlation (analyze graphs at correlation
      cutoffs)] [-div <num> (cluster size separating value)] [-report-scale
      <num> (edge weight/threshold scaling)] [--dim (report native format and
      dimensions)] [-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
      permissive threshold. For example, one can create a graph from array
      expression data using mcxarray with a very low pearson correlation
      cutoff 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
      connected 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
      purpose 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)
        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                          mcx q(1)
