f.extract.ff.numeric

This function returns the requested columns and/or rows and converts it to a numeric matrix (by default, the extraction from an ff matrix with defined levels returns a factor vector).

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.extract.ff.numeric function

<dl><dt>gen.data</dt>
<dd>The ff matrix with genetic data.</dd>
<dt>cols</dt>
<dd>The sequence numbering the columns which are to be retrieved, if NULL (default) then all the columns will be extracted.</dd>
<dt>rows</dt>
<dd>The sequence numbering the rows which are to be retrieved, if NULL (default) then all the rows will be extracted.</dd></dl>

Arguments

Extract a part of an ff array (matrix) and return it as numeric matrix — f.extract.ff.numeric

<dl>

<dt>gen.data</dt>
<dd>The ff matrix with genetic data.</dd>


<dt>cols</dt>
<dd>The sequence numbering the columns which are to be retrieved, if NULL (default) then all the columns will be extracted.</dd>


<dt>rows</dt>
<dd>The sequence numbering the rows which are to be retrieved, if NULL (default) then all the rows will be extracted.</dd>

</dl>

f.extract.ff.numeric: Extract a part of an ff array (matrix) and return it as numeric matrix

Description

Usage

Value

Arguments