NAME
Bio::PopGen::HtSNP.pm- Select htSNP from a haplotype set
SYNOPSIS
use Bio::PopGen::HtSNP;
my $obj = Bio::PopGen::HtSNP->new($hap,$snp,$pop);DESCRIPTION
Select the minimal set of SNP that contains the full information about the haplotype without redundancies.
Take as input the followin values:
- - the haplotype block (array of array).
- - the snp id (array).
- - family information and frequency (array of array).
The final haplotype is generated in a numerical format and the SNP's sets can be retrieve from the module.
considerations:
- If you force to include a family with indetermination, the SNP's with indetermination will be removed from the analysis, so consider before to place your data set what do you really want to do.
- If two families have the same information (identical haplotype), one of them will be removed and the removed files will be stored classify as removed.
- Only are accepted for calculation A, C, G, T and - (as deletion) and their combinations. Any other value as n or ? will be considered as degenerations due to lack of information.
RATIONALE
On a haplotype set is expected that some of the SNP and their variations contribute in the same way to the haplotype. Eliminating redundancies will produce a minimal set of SNP's that can be used as input for a taging selection process. On the process SNP's with the same variation are clustered on the same group.
The idea is that because the tagging haplotype process is exponential. All redundant information we could eliminate on the tagging process will help to find a quick result.
CONSTRUCTORS
my $obj = Bio::PopGen::HtSNP->new
(-haplotype_block => \@haplotype_patterns,
-snp_ids => \@snp_ids,
-pattern_freq => \@pattern_name_and_freq);where $hap, $snp and $pop are in the format:
my $hap = [
'acgt',
'agtc',
'cgtc'
]; # haplotype patterns' id
my $snp = [qw/s1 s2 s3 s4/]; # snps' Id's
my $pop = [
[qw/ uno 0.20/],
[qw/ dos 0.20/],
[qw/ tres 0.15/],
]; # haplotype_pattern_id FrequencyOBJECT METHODS
See Below for more detailed summaries.DETAILS
How the process is working with one example
Let's begin with one general example of the code.
Input haplotype:
acgtcca-t
cggtagtgc
cccccgtgc
cgctcgtgcThe first thing to to is to split the haplotype into characters.
a c g t c c a - t
c g g t a g t g c
c c c c c g t g c
c g c t c g t g cNow we have to convert the haplotype to Upercase. This will produce the same SNP if we have input a or A.
A C G T C C A - T
C G G T A G T G C
C C C C C G T G C
C G C T C G T G CThe program admit as values any combination of ACTG and - (deletions). The haplotype is converted to number, considering the first variation as zero and the alternate value as 1 (see expanded description below).
0 0 0 0 0 0 0 0 0
1 1 0 0 1 1 1 1 1
1 0 1 1 0 1 1 1 1
1 1 1 0 0 1 1 1 1Once we have the haplotype converted to numbers we have to generate the snp type information for the haplotype.
SNP code = SUM ( value * multiplicity ^ position );
where:
SUM is the sum of the values for the SNP
value is the SNP number code (0 [generally for the mayor allele],
1 [for the minor allele].
position is the position on the block.For this example the code is:
0 0 0 0 0 0 0 0 0
1 1 0 0 1 1 1 1 1
1 0 1 1 0 1 1 1 1
1 1 1 0 0 1 1 1 1
------------------------------------------------------------------
14 10 12 4 2 14 14 14 14
14 = 0*2^0 + 1*2^1 + 1*2^2 + 1*2^3
12 = 0*2^0 + 1*2^1 + 0*2^2 + 1*2^3
....Once we have the families classify. We will take just the SNP's not redundant.
14 10 12 4 2This information will be passed to the tag module is you want to tag the htSNP.
Whatever it happens to one SNPs of a class will happen to a SNP of the same class. Therefore you don't need to scan redundancies
Working with fuzzy data.
This module is designed to work with fuzzy data. As the source of the haplotype is diverse. The program assume that some haplotypes can be generated using different values. If there is any indetermination (? or n) or any other degenerated value or invalid. The program will take away This SNP and will leave that for a further analysis.
On a complex situation:
a c g t ? c a c t
a c g t ? c a - t
c g ? t a g ? g c
c a c t c g t g c
c g c t c g t g c
c g g t a g ? g c
a c ? t ? c a c tOn this haplotype everything is happening. We have a multialelic variance. We have indeterminations. We have deletions and we have even one SNP which is not a real SNP.
The buiding process will be the same on this situation.
Convert the haplotype to uppercase.
A C G T ? C A C T
A C G T ? C A - T
C G ? T A G ? G C
C A C T C G T G C
C G C T C G T G C
C G G T A G ? G C
A C ? T ? C A C TAll columns that present indeterminations will be removed from the analysis on this Step.
hapotype after remove columns:
A C T C C T
A C T C - T
C G T G G C
C A T G G C
C G T G G C
C G T G G C
A C T C C TAll changes made on the haplotype matrix, will be also made on the SNP list.
snp_id_1 snp_id_2 snp_id_4 snp_id_6 snp_id_8 snp_id_9now the SNP that is not one SNP will be removed from the analysis. SNP with Id snp_id_4 (the one with all T's).
because of the removing. Some of the families will become the same and will be clustered. A posteriori analysis will diference these families. but because of the indetermination can not be distinguish.
A C C C T
A C C - T
C G G G C
C A G G C
C G G G C
C G G G C
A C C C TThe result of the mergering will go like:
A C C C T
A C C - T
C G G G C
C A G G COnce again the changes made on the families and we merge the frequency (to be implemented)
Before to convert the haplotype into numbers we consider how many variations we have on the set. On this case the variations are 3.
The control code will use on this situation base three as mutiplicity
0 0 0 0 0
0 0 0 1 0
1 1 1 2 1
1 2 1 2 1
-----------------------------------
36 63 36 75 36And the minimal set for this combination is
0 0 0
0 0 1
1 1 2
1 2 2NOTE: this second example is a remote example an on normal conditions. This conditions makes no sense, but as the haplotypes, can come from many sources we have to be ready for all kind of combinations.
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 listsSupport
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
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Function: constructor of the class.
Usage : $obj-> Bio::PopGen::HtSNP->new(-haplotype_block
-snp_ids
-pattern_freq)
Returns : self hash
Args : input haplotype (array of array)
snp_ids (array)
pop_freq (array of array)
Status : publichaplotype_block
Title : haplotype_block
Usage : my $haplotype_block = $HtSNP->haplotype_block();
Function: Get the haplotype block for a haplotype tagging selection
Returns : reference of array
Args : reference of array with haplotype pattern snp_ids
Title : snp_ids
Usage : my $snp_ids = $HtSNP->$snp_ids();
Function: Get the ids for a haplotype tagging selection
Returns : reference of array
Args : reference of array with SNP idspattern_freq
Title : pattern_freq
Usage : my $pattern_freq = $HtSNP->pattern_freq();
Function: Get the pattern id and frequency for a haplotype
tagging selection
Returns : reference of array
Args : reference of array with SNP ids_check_input
Title : _check_input
Usage : _check_input($self)
Function: check for errors on the input
Returns : self hash
Args : self
Status : internal_haplotype_length_error
Title : _haplotype_length_error
Usage : _haplotype_length_error($self)
Function: check if the haplotype length is the same that the one on the
SNP id list. If not break and exit
Returns : self hash
Args : self
Status : internal_population_error
Title : _population_error
Usage : _population_error($self)
Function: use input_block and pop_freq test if the number of elements
match. If doesn't break and quit.
Returns : self hash
Args : self
Status : internal_do_it
Title : _do_it
Usage : _do_it($self)
Function: Process the input generating the results.
Returns : self hash
Args : self
Status : internalinput_block
Title : input_block
Usage : $obj->input_block()
Function: returns input block
Returns : reference to array of array
Args : none
Status : publichap_length
Title : hap_length
Usage : $obj->hap_length()
Function: get numbers of SNP on the haplotype
Returns : scalar
Args : none
Status : publicpop_freq
Title : pop_freq
Usage : $obj->pop_freq()
Function: returns population frequency
Returns : reference to array
Args : none
Status : publicdeg_snp
Title : deg_snp
Usage : $obj->deg_snp()
Function: returns snp_removes due to indetermination on their values
Returns : reference to array
Args : none
Status : publicsnp_type
Title : snp_type
Usage : $obj->snp_type()
Function: returns hash with SNP type
Returns : reference to hash
Args : none
Status : publicsilent_snp
Title : silent_snp
Usage : $obj->silent_snp()
Function: some SNP's are silent (not contibuting to the haplotype)
and are not considering for this analysis
Returns : reference to a array
Args : none
Status : publicuseful_snp
Title : useful_snp
Usage : $obj->useful_snp()
Function: returns list of SNP's that are can be used as htSNP. Some
of them can produce the same information. But this is
not considered here.
Returns : reference to a array
Args : none
Status : publicht_type
Title : ht_type
Usage : $obj->ht_type()
Function: every useful SNP has a numeric code dependending of its
value and position. For a better description see
description of the module.
Returns : reference to a array
Args : none
Status : publicht_set
Title : ht_set
Usage : $obj->ht_set()
Function: returns the minimal haplotype in numerical format. This
haplotype contains the maximal information about the
haplotype variations but with no redundancies. It's the
minimal set that describes the haplotype.
Returns : reference to an array of arrays
Args : none
Status : publicsnp_type_code
Title : snp_type_code
Usage : $obj->snp_type_code()
Function: returns the numeric code of the SNPs that need to be
tagged that correspond to the SNP's considered in ht_set.
Returns : reference to an array
Args : none
Status : publicsnp_and_code
Title : snp_and_code
Usage : $obj->snp_and_code()
Function: Returns the full list of SNP's and the code associate to
them. If the SNP belongs to the group useful_snp it keep
this code. If the SNP is silent the code is 0. And if the
SNP is degenerated the code is -1.
Returns : reference to an array of array
Args : none
Status : publicdeg_pattern
Title : deg_pattern
Usage : $obj->deg_pattern()
Function: Returns the a list with the degenerated haplotype.
Sometimes due to degeneration some haplotypes looks
the same and if we don't remove them it won't find
any tag.
Returns : reference to a hash of array
Args : none
Status : publicsplit_hap
Title : split_hap
Usage : $obj->split_hap()
Function: simple representation of the haplotype base by base
Same information that input haplotype but base based.
Returns : reference to an array of array
Args : none
Status : public_split_haplo
Title : _split_haplo
Usage : _split_haplo($self)
Function: Take a haplotype and split it into bases
Returns : self
Args : none
Status : internal_to_upper_case
Title : _to_upper_case
Usage : _to_upper_case()
Function: make SNP or in-dels Upper case
Returns : self
Args : an AoA ref
Status : private_remove_deg
Title : _remove_deg
Usage : _remove_deg()
Function: when have a indetermination or strange value this SNP
is removed
Returns : haplotype family set and degeneration list
Args : ref to an AoA and a ref to an array
Status : internal_rem_silent_snp
Title : _rem_silent_snp
Usage : _rem_silent_snp()
Function: there is the remote possibilty that one SNP won't be a
real SNP on this situation we have to remove this SNP,
otherwise the program won't find any tag
Returns : nonthing
Args : ref to an AoA and a ref to an array
Status : internal_find_silent_snps
Title : _find_silent_snps
Usage :
Function: list of snps that are not SNPs. All values for that
SNPs on the set is the same one. Look stupid but can
happend and if this happend you will not find any tag
Returns : nothing
Args :
Status :_find_indet
Title : _find_indet
Usage :
Function: find column (SNP) with invalid or degenerated values
and store this values into the second parameter supplied.
Returns : nothing
Args : ref to AoA and ref to an array
Status : internal_remove_col
Title : _remove_col
Usage :
Function: remove columns contained on the second array from
the first arr
Returns : nothing
Args : array of array reference and array reference
Status : internal_remove_snp_id
Title : _remove_snp_id
Usage :
Function: remove columns contained on the second array from
the first arr
Returns : nothing
Args : array of array reference and array reference
Status : internal_find_deg_pattern
Title : _find_deg_pattern
Usage :
Function: create a list with the degenerated patterns
Returns : @array
Args : a ref to AoA
Status : public_keep_these_patterns
Title : _keep_these_patterns
Usage :
Function: this is a basic approach, take a LoL and a list,
keep just the columns included on the list
Returns : nothing
Args : an AoA and an array
Status : publiccompare_arrays
Title : compare_arrays
Usage :
Function: take two arrays and compare their values
Returns : 1 if the two values are the same
0 if the values are different
Args : an AoA and an array
Status : public_convert_to_numbers
Title : _convert_to_numbers
Usage : _convert_to_numbers()
Function: tranform the haplotype into numbers. before to do that
we have to consider the variation on the set.
Returns : nonthing
Args : ref to an AoA and a ref to an array
Status : internal_snp_type_code
Title : _snp_type_code
Usage :
Function:
we have to create the snp type code for each version.
The way the snp type is created is the following:
we take the number value for every SNP and do the
following calculation
let be a SNP set as follow:
0 0
1 1
1 2
and multiplicity 3
on this case the situation is:
sum (value * multiplicity ^ position) for each SNP
0 * 3 ^ 0 + 1 * 3 ^ 1 + 1 * 3 ^ 2 = 12
0 * 3 ^ 0 + 1 * 3 ^ 1 + 2 * 3 ^ 2 = 21
Returns : nothing
Args : $self
Status : private_alleles_number
Title : _alleles_number
Usage :
Function: calculate the max number of alleles for a haplotype and
if the number. For each SNP the number is stored and the
max number of alleles for a SNP on the set is returned
Returns : max number of alleles (a scalar storing a number)
Args : ref to AoA
Status : public_htSNP
Title : _htSNP
Usage : _htSNP()
Function: calculate the minimal set that contains all information of the
haplotype.
Returns : nonthing
Args : ref to an AoA and a ref to an array
Status : internal_snp_and_code_summary
Title : _snp_and_code_summary
Usage : _snp_and_code_summary()
Function: compile on a list all SNP and the code for each. This
information can be also obtained combining snp_type and
snp_type_code but on these results the information about
the rest of SNP's are not compiled as table.
0 will be silent SNPs
-1 are degenerated SNPs
and the rest of positive values are the code for useful SNP
Returns : nonthing
Args : ref to an AoA and a ref to an array
Status : internal