package SGN::View::Mason::Commands;
use strict;
use vars qw($m $c);
HTML::Mason::Component::FileBased->new(
'code' => sub {
use utf8; local $SGN::View::Mason::Commands::m = $HTML::Mason::Commands::m;
$m->debug_hook( $m->current_comp->path ) if ( HTML::Mason::Compiler::IN_PERL_DB() );

#line 14 "/home/production/cxgn/sgn/mason/qtl/submission/guide/statistics.mas"
$m->print( '
' );
#line 15 "/home/production/cxgn/sgn/mason/qtl/submission/guide/statistics.mas"
$m->comp( { content => sub {
#line 19 "/home/production/cxgn/sgn/mason/qtl/submission/guide/statistics.mas"
$m->print( '


The qtl analysis uses R/QTL package and implements an interval mapping with the following parameters. <br/>

<ul>
  <li>
    <strong>QTL model:</strong> Select the one dimension single QTL genome scan&nbsp; (the two-dimension two genome QTL scan is under development)
  </li>
  <li>
    <strong>QTL mapping method:</strong> You can select&nbsp; \'Single Marker Analysis\'&nbsp; or \'Maximum Likelihood\' for standard interval mapping or for an approximation of it \'Haley-Knot Regression\' or \'Multiple Imputation\'. Use \'Multiple Imputation\' only if you want to estimate the QTL genotype based on random imputation.
  </li>
  <li>
    <strong>QTL genotype probability method:</strong> Select \'Calculate\' if you want the QTL genotype to be estimated based the observed marker data. This method must be selected if you selected \'Maximum Likelihood\' or \'Haley-Knot Regression\'. If you selected \'Multiple Imputation\' then choose the \'Simulate\' method.
  </li>
  <li>
    <strong>Genotype probability significance level:</strong> select the genotyping error rate you want to allow.
  </li>
  <li>
    <strong>Genome scan size (cM):</strong> select the genome size (interval) you want the QTL genotype probabilities to be calculated.
  </li>
  <li>
    <strong>No. of imputations:</strong> applicable only for \'Multiple Imputation\' mapping method and \'Simulate\' QTL genotype probability method. 
  </li>
  <li>
    <strong>No. of permutations and significance level:</strong> select the number of permutations to perform and the error rate for the calculation of the LOD threshold.
  </li>
</ul>

' );
#line 48 "/home/production/cxgn/sgn/mason/qtl/submission/guide/statistics.mas"
} }, '/page/info_section.mas', 
   title      => "Step 5: Statistical parameters",
  collapsible => 1,
  collapsed   => 1
 );
#line 48 "/home/production/cxgn/sgn/mason/qtl/submission/guide/statistics.mas"
$m->print( '
' );
;return;
},
'load_time' => 1763134725,

)
;