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 Frequency
OBJECT 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
cgctcgtgc
The 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 c
Now 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 C
The 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 1
Once 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 2
This 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 t
On 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 T
All 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 T
All 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_9
now 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 T
The 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 C
Once 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 36
And the minimal set for this combination is
0 0 0
0 0 1
1 1 2
1 2 2
NOTE: 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 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://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 : public
haplotype_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 ids
pattern_freq¶
Title : pattern_freq
Usage : my $pattern_freq = $HtSNP->pattern_freq();
Function: Get the pattern id and frequency for a haplotype
tagging selection
Returns : reference of array
Args : reference of array with SNP ids
Title : _check_input
Usage : _check_input($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 : internal
Title : input_block
Usage : $obj->input_block()
Function: returns input block
Returns : reference to array of array
Args : none
Status : public
hap_length¶
Title : hap_length
Usage : $obj->hap_length()
Function: get numbers of SNP on the haplotype
Returns : scalar
Args : none
Status : public
pop_freq¶
Title : pop_freq
Usage : $obj->pop_freq()
Function: returns population frequency
Returns : reference to array
Args : none
Status : public
deg_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 : public
snp_type¶
Title : snp_type
Usage : $obj->snp_type()
Function: returns hash with SNP type
Returns : reference to hash
Args : none
Status : public
silent_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 : public
useful_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 : public
ht_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 : public
ht_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 : public
snp_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 : public
snp_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 : public
deg_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 : public
split_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 : public
compare_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