Bio::PopGen::TagHaplotype.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::PopGen::TagHaplotype.pm - Haplotype tag object.

SYNOPSIS

     use Bio::PopGen::TagHaplotype;
 
     my $obj = Bio::PopGen::TagHaplotype -> new($hap);
 
 

DESCRIPTION

This module take as input a haplotype and try toe get the minimal set of SNP that define the haplotype. This module can be use alone. But due to the tagging haplotype process is exponential one. My suggestion is that before to use this module you pass your data under Select.mp module also on this folder. In any case if, you provide an haplotype the module will try to find the answer to your question.

CONSTRUCTORS

     my $obj = Bio::PopGen::TagHaplotype -> new($hap);
 
     were $hap is the reference to an array of array with the haplotype.
 
     $hap= [[0, 0, 0],
            [1, 0, 0],
            [0, 1, 1]
           ];
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Pedro M. Gomez-Fabre

Email pgf18872-at-gsk-dot-com

new

  Title   : new
  Function: constructor of the class.
  Returns : self hash
  Args    : input haplotype (array of array)
  Status  : public
 
 

haplotype_block

  Title   : haplotype_block
  Usage   : my $haplotype_block = $TagHaplotype->haplotype_block();
  Function: Get the haplotype block for a haplotype tagging selection
  Returns : reference of array
  Args    : reference of array with haplotype pattern
 
 

input_block

  Title   : input_block 
  Usage   : $obj->input_block()
  Function: returns haplotype block. By now will produce the same ouput than
            $self->haplotype_block. but for compatiblity, this method is kept. 
            This method is deprecated.
  Returns : reference to array of array with the haplotype input value 
  Args    : none 
  Status  : public
 
 

tag_list

  Title   : tag_list 
  Usage   : $obj->tag_list()
  Function: returns the list of SNPs combination that identify the
            haplotype. All combinations are displayed as arrays
  Returns : reference to array of array. 
  Args    : none
  Status  : public
 
 

tag_length

  Title   : tag_length 
  Usage   : $obj->tag_length()
  Function: returns the length of the tag.
  Returns : scalar 
  Args    : none
  Status  : public
 
 

_scan_snp

  Title   : _scan_snp 
  Usage   : internal
  Function: scan sets increasing the length until find a non degenerated
            pattern. 
  Returns : scalar
  Args    : none
  Status  : private
 
 

_gen_comb

  Title   : _gen_comb 
  Usage   : internal
  Function: we supply the length of the haplotype and the length of the
            word we need to find and the functions returns the possible
            list of combinations.
  Returns : scalar
  Args    : none
  Status  : private
 
 

_generateCombinations

  Title   : _generateCombinations 
  Usage   : internal
  Function: Recursive function that produce all combinations for a set
 
            i.e.:
 
            1, 2, 3, 4
 
            and word of B<3> will produce:
 
            1, 2, 3
            1, 2, 4
            1, 3, 4
            2, 3, 4
 
  Returns :
  Args    : none
  Status  : private
 
 

_scan_combinations

  Title   : _scan_combinations 
  Usage   : internal
  Function: take the haplotype and a list of possible combination
            for that length. Generate a subset and scan it to find if
            the information is enought to define the haplotype set.
  Returns :
  Args    : none
  Status  : private