f.create.snp.names

Creating column names either from a .map file or generating dummy names

internal

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

f.create.snp.names function

<dl><dt>map.file</dt>
<dd>Filename (with path if the file is not in current directory) of the
.map file holding the SNP names, if available (see Details).</dd>
<dt>header</dt>
<dd>Logical: does the map.file contain a header in the first row?
Default: FALSE.</dd>
<dt>ncol</dt>
<dd>Number of columns IN TOTAL in the dataset containing only the genotype data</dd>
<dt>format</dt>
<dd>Format of data (will influence how data is processed) - choose from:<ul>
<li>haplin - data already in one row per family,</li>
<li>ped - data from .ped file, each row represents an individual.</li>
</ul>.</dd>
<dt>design</dt>
<dd>The design used in the study - choose from:<ul>
<li>triad - (default), 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></dl>

Arguments

Intern function for creating column names for genotype data — f.create.snp.names

<dl>

<dt>map.file</dt>
<dd>Filename (with path if the file is not in current directory) of the
.map file holding the SNP names, if available (see Details).</dd>


<dt>header</dt>
<dd>Logical: does the map.file contain a header in the first row?
Default: FALSE.</dd>


<dt>ncol</dt>
<dd>Number of columns IN TOTAL in the dataset containing only the genotype data</dd>


<dt>format</dt>
<dd>Format of data (will influence how data is processed) - choose from:<ul>
<li>haplin - data already in one row per family,</li>
<li>ped - data from .ped file, each row represents an individual.</li>
</ul>.</dd>


<dt>design</dt>
<dd>The design used in the study - choose from:<ul>
<li>triad - (default), 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>

</dl>

f.create.snp.names: Intern function for creating column names for genotype data

Description

Usage

Value

Arguments

Details