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  : 

cpanm Genetics

perl -MCPAN -e shell
install Genetics