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
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bioperl-l@bioperl.org - General discussion
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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)