Delila Program: compan

compan program

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

{   version = 3.26;  (* of compan.p 2015 Apr 26}

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

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

files
      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;

description
      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 'uncertainty' of the composition is also calculated,
      using the standard information theory definition:
         H = -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 uncertainty
      in bits.  (Note: This was called 'information by Gary Stormo
      originally.  However it is not the information, it is the uncertainty.)

see also
      comp.p

author
      Gary Stormo, corrected by Thomas Schneider

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