showGen

This is a help function to extract genotypes from an object read in with
 genDataRead (or loaded with genDataLoad).

Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".

Hakon Gjessing

Haplin

Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes

Hakon K. Gjessing

Miriam Gjerdevik

Julia Romanowska

Oivind Skare

showGen function

<dl><dt>data.in</dt>
<dd>The data read in by genDataRead.</dd>
<dt>design</dt>
<dd>The design used in the study - choose from:<ul>
<li>triad - data includes genotypes of mother, father and child;</li>
<li>cc - classical case-control;</li>
<li>cc.triad - hybrid design: triads with cases and controls;</li>
</ul>.</dd>
<dt>n</dt>
<dd>Number of rows to display or "all" (default: 5).</dd>
<dt>from</dt>
<dd>From which row to display (optional, default: from the first).</dd>
<dt>to</dt>
<dd>To which row to display (optional).</dd>
<dt>sex</dt>
<dd>If the sex column is part of the phenotypic information, the user can
choose based on one of the categories used in this column (optional);
NB: this does not combine with the 'to' and 'from' arguments.</dd>
<dt>markers</dt>
<dd>A vector specifying which markers to display or "all" (default: first
5); NB: the user can specify the markers by numbers or by their names.</dd></dl>

Arguments

Display chosen genotypes — showGen

<dl>

<dt>data.in</dt>
<dd>The data read in by genDataRead.</dd>


<dt>design</dt>
<dd>The design used in the study - choose from:<ul>
<li>triad - data includes genotypes of mother, father and child;</li>
<li>cc - classical case-control;</li>
<li>cc.triad - hybrid design: triads with cases and controls;</li>
</ul>.</dd>


<dt>n</dt>
<dd>Number of rows to display or "all" (default: 5).</dd>


<dt>from</dt>
<dd>From which row to display (optional, default: from the first).</dd>


<dt>to</dt>
<dd>To which row to display (optional).</dd>


<dt>sex</dt>
<dd>If the sex column is part of the phenotypic information, the user can
choose based on one of the categories used in this column (optional);
NB: this does not combine with the 'to' and 'from' arguments.</dd>


<dt>markers</dt>
<dd>A vector specifying which markers to display or "all" (default: first
5); NB: the user can specify the markers by numbers or by their names.</dd>

</dl>

showGen: Display chosen genotypes

Description

Usage

Value

Arguments