Delila Program: compan

compan program

Documentation for the compan program is below, with links to related programs in the "see also" section.

{version = 3.25;  (* of compan.p 2001 Mar 26}

(* begin module describe.compan *)
      compan: composition analysis.

      compan(cmp: in, anal: out, companp: in, output: out)

      cmp: the input composition, which is the output of program comp;
      anal: the output analysis of this program;
      companp: for parameters; should contain a single integer which specifies
         the maximum level for which the composition is analyzed.  the
         maximum allowed level is 4, or the maximum level for which the
         composition was determined.
      output: for user messages;

      calculates chi squared from a composition using:
         1) assumption of equal frequencies to calculate mono, di, tri
            and tet expecteds;
         2) mono frequencies to calculate di, tri  and tet expecteds;
         3) di frequencies to calculate tri and tet expecteds;
         4) tri frequencies to calculate tet expecteds;
      the partial chi squared values are given for each oligo.
      the 'information' content of the composition is also calculated,
      using the standard information theory definition:
         information = -sum(frequency * log(frequency)),
      where the sum is over each oligonucleotide of a given length
      and the log is taken to the base 2.  this gives the information
      in bits.

see also

      gary stormo

      the program cannot do calculations for compositions larger than 4
(* end module describe.compan *)
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