table of contents
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://github.com/bioperl/bioperl-live/issues
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
2018-10-27 | perl v5.26.2 |