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
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