toyped

Toy pedigree with 4 individuals typed at 1 SNP marker. Individual 1 is missing one allele.

datasets

A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the MERLIN software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the Familias software can be imported and analysed in paramlink. Finally, paramlink offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the kinship2 package).

Magnus Dehli Vigeland

paramlink

Parametric Linkage and Other Pedigree Analysis in R

toyped function

A data frame with one row for each individual, and the following columns:<dl class="dl-horizontal">
 <dt><code>FAMID</code></dt><dd>family id</dd>
 <dt><code>ID</code></dt><dd>individual id</dd>
 <dt><code>FID</code></dt><dd>father id (0 if founder)</dd>
 <dt><code>MID</code></dt><dd>mother id (0 if founder)</dd>
 <dt><code>SEX</code></dt><dd>sex: male=1, female=2</dd>
 <dt><code>AFF</code></dt><dd>affection status: healthy=1, affected=2, unknown=0</dd>
 <dt><code>M_A1</code></dt><dd>first marker, first allele</dd>
 <dt><code>M_A2</code></dt><dd>first marker, second allele</dd>
 </dl>

Format

Toy pedigree for linkage analysis — toyped

A data frame with one row for each individual, and the following columns:<dl class='dl-horizontal'>
 <dt><code>FAMID</code></dt><dd>family id</dd>
 <dt><code>ID</code></dt><dd>individual id</dd>
 <dt><code>FID</code></dt><dd>father id (0 if founder)</dd>
 <dt><code>MID</code></dt><dd>mother id (0 if founder)</dd>
 <dt><code>SEX</code></dt><dd>sex: male=1, female=2</dd>
 <dt><code>AFF</code></dt><dd>affection status: healthy=1, affected=2, unknown=0</dd>
 <dt><code>M_A1</code></dt><dd>first marker, first allele</dd>
 <dt><code>M_A2</code></dt><dd>first marker, second allele</dd>
 </dl>

toyped: Toy pedigree for linkage analysis

Description

Usage

Arguments

Format

Details

Examples