Delila Program: compan
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compan program

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

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**{version = 3.25; (* of compan.p 2001 Mar 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 '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
comp.p
author
gary stormo
bugs
the program cannot do calculations for compositions larger than 4
*)
(* end module describe.compan *)
{This manual page was created by makman 1.44}
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