Method 
markov 
 
Classpackage  
G::Seq::Markov 
 
 
Function 
  Calculates the Markov analysis for all oligomers of specified length. 
 
 
Description 
  This method calculates the Markov analysis for all oligomers of specified length. 
The returned value is a reference to a hash with keys as oligomer  
 sequences, and values as the O/E values at (length - 2) order Markov. 
Option -length sets the length of the oligomer to analyze.  -mincount sets the minimum number of oligomer count to report.  -filename sets the output filename, and -output determines the output format ("f" for file, and "stdout" for STDOUT output) 
 
 
Requirements 
modules   
 SubOpt.pm 
 
applications 
none 
 
data 
none 
 
Parameters 
essential 
 
first     pointer  G instance     G's instance 
 
 
 
option 
length     int     length_oligomer         default=6 
mincount   int     min_oligomer            default=10 
filename   string  filename                default="markov.csv" 
option     string  [f or stdout]           default="stdout" 
 
Returns 
first      pointer      hash_of_O/E_values     Eeference to a hash with keys as oligomer sequences(values are the O/E values at (length - 2) order Markov.) 
 
 
Usage 
(pointer hash_of_O/E_values) = &markov(pointer G instance, -length=>6, -mincount=>10, -filename=>'markov.csv',-output=>'stdout');  
 
Input file  
none 
 
 
Output file  
none 
 
References 
none  
 
Comments 
none 
 
Authors 
This method was written by Kazuharu Arakawa(gaou@g-language.org) at Institute for Advanced Biosciences Keio Univ.  
 
 
History 
Written 30 August  2001 - Kazuharu Arakawa