Bio::PopGen::TagHaplotype(3pm)				User Contributed Perl Documentation			    Bio::PopGen::TagHaplotype(3pm)

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:

	 https://redmine.open-bio.org/projects/bioperl/

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 output 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

perl v5.14.2							    2012-03-02					    Bio::PopGen::TagHaplotype(3pm)