Analysis.pm

- NAME
- SYNOPSIS
- DESCRIPTION
- LICENSE
- FEEDBACK
- AUTHOR - Steve Mathias
- DETAILS
- Imported Packages
- Inheritance
- Public Methods

- chiSquareAssocTest
- graphAlleleFreqs
- calculateHet
- calculateSnpHW

# NAME

Genetics::API::Analysis

# SYNOPSIS

      # The following code will produce a graph of allele frequencies in two
      # different Subject Clusters

      $affCluster = $api->getObject({TYPE => "Cluster", NAME => "HT Affecteds"}) ;
      $unaffCluster = $api->getObject({TYPE => "Cluster", NAME => "Normals"}) ;

      $marker = $api->getObject({TYPE => "Marker", NAME => "agtT174M"}) ;

      $api->graphAlleleFreqs(
                             MARKER => $marker,
                             FREQSOURCES => [ $affCluster, $unaffCluster ],
                             ALLELETYPE => "Nucleotide"
                            ) ;

      # The following code will perform a chi-square test on this same data

      $api->chiSquareAssocTest(
                               MARKER => $marker,
                               SC1 => $affCluster,
                               SC2 => $unaffCluster,
                               ALLELETYPE => "Nucleotide",
                              ) ;

# DESCRIPTION

This package contains methods for the analysis of data contained in GenPerl objects. Also see Genetics::API::Analysis::Linkage for methods relating to genetic linkage analyses.

# LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

# FEEDBACK

Currently, all feedback should be sent directly to the author.

# AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

Address: Genomica Corporation 1745 38th Street Boulder, CO 80301

# DETAILS

The rest of the documentation describes each of the object variables and methods. The names of internal variables and methods are preceded with an underscore (_).

# Imported Packages

     strict             Just to be anal
     vars               Global variables
     Carp               Error reporting
     GD::Graph::bars    Graphing allele frequencies
     GD::Graph::colour  Graphing allele frequencies
     GD::Graph::Data    Graphing allele frequencies

# Inheritance

     Exporter           Make methods available to importing packages

# Public Methods

sub test { `my($self)` = @_ ; my($sth, $aoaRef) ; my $dbh = $self->{dbh} ;

      $sth = $dbh->prepare( "select alleleCallID from AlleleCall
                       where gtID = 4009
                       and alleleID = 26" ) ;
      $sth->execute() ;
      $aoaRef = $sth->fetchall_arrayref() ;
      print scalar(@$aoaRef), "\n" ;

      return(1) ;
    }

## chiSquareAssocTest

      Function  : Perform a simple chi-square association test.
      Arguments : A Marker object, a string containing an allele type and two
                  Subject Cluster objects.
      Returns   : N/A
      Scope     : Public
      Called by :
      Comments  :

## graphAlleleFreqs

      Function  : Graph the allele frequencies for a Marker in a group of Subjects.
      Arguments : A hash of parameters as follows
                  MARKER => The Marker object whose allele frequencies are to be graphed.
                            Required, for obvious reasons.
                  FREQSOURCES => Array pointer to a list of Cluster (Kindred or Subject)
                                 and/or FrequencySource objects.
                                 The source(s) for allele frequencies.
                                 Required, for obvious reasons.
                  ALLELETYPE => The type of alleles whose frequencies are to be graphed.
                                Optional, the default value is "Code".
      Returns   : N/A
      Scope     : Public
      Comments  : Calls xv to display the graphic.

## calculateHet

     Function  : Calculate the heterozygosity for a Marker or SNP.
     Arguments : A Marker object, a string containing an allele type, and one of
                  the following defining the Subject group:
                    - a Subject Cluster object
                    - an array reference to a list of Subject objects
                    - a Kindred Cluster object
                    - an array reference to a list of Kindred objects
     Returns   : A scalar float
     Scope     : Public
     Comments  : Arguments are passed directly to API::DB::Query::getAlleleFreqs()

## calculateSnpHW

     Function  :
     Arguments :
     Returns   :
     Example   : calculateHW()
     Scope     :
     Comments  :