Provided by: libbio-perl-perl_1.7.2-3_all
Bio::PopGen::TagHaplotype.pm - 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 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.
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 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 compatibility, 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 enough to define the haplotype set. Returns : Args : none Status : private