Christopher Fields > BioPerl > Bio::PopGen::TagHaplotype



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NAME ^ - Haplotype tag object.


    use Bio::PopGen::TagHaplotype;

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


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 module also on this folder. In any case if, you provide an haplotype the module will try to find the answer to your question.


    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]


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AUTHOR - Pedro M. Gomez-Fabre ^

Email pgf18872-at-gsk-dot-com


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


 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


 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


 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


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


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


 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


 Title   : _generateCombinations 
 Usage   : internal
 Function: Recursive function that produce all combinations for a set


           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


 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
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