allGenotypes

fast.grid

geno.grid.subset

Auxiliary functions computing possible genotype combinations in a pedigree.
These are not normally intended for end users.

NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PEDSUITE'
PACKAGES (<https://magnusdv.github.io/pedsuite/>). 'PARAMLINK' IS
MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW
PROJECTS. 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 Vigeland

paramlink

Parametric Linkage and Other Pedigree Analysis in R

Magnus Dehli Vigeland

Thore Egeland

Guro Doerum

allGenotypes function

<dl><dt>n</dt>
<dd>a positive integer.</dd>
<dt>argslist</dt>
<dd>a list of vectors.</dd>
<dt>as.list</dt>
<dd>if TRUE, the output is a list, otherwise a matrix.</dd>
<dt>x</dt>
<dd>a <code>linkdat</code> object.</dd>
<dt>partialmarker</dt>
<dd>a <code>marker</code> object compatible with <code>x</code>.</dd>
<dt>ids</dt>
<dd>a numeric with ID labels of one or more pedigree members.</dd>
<dt>chrom</dt>
<dd>a character, either 'X' or 'AUTOSOMAL'. If missing, the 'chrom'
attribute of <code>partialmarker</code> is used. If this is also missing, then
'AUTOSOMAL' is taken as the default value.</dd>
<dt>make.grid</dt>
<dd>a logical. If FALSE, a list is returned, otherwise
<code>fast.grid</code> is applied to the list before returning it.</dd></dl>

Arguments

Genotype combinations — allGenotypes

<dl>

<dt>n</dt>
<dd>a positive integer.</dd>


<dt>argslist</dt>
<dd>a list of vectors.</dd>


<dt>as.list</dt>
<dd>if TRUE, the output is a list, otherwise a matrix.</dd>


<dt>x</dt>
<dd>a <code>linkdat</code> object.</dd>


<dt>partialmarker</dt>
<dd>a <code>marker</code> object compatible with <code>x</code>.</dd>


<dt>ids</dt>
<dd>a numeric with ID labels of one or more pedigree members.</dd>


<dt>chrom</dt>
<dd>a character, either 'X' or 'AUTOSOMAL'. If missing, the 'chrom'
attribute of <code>partialmarker</code> is used. If this is also missing, then
'AUTOSOMAL' is taken as the default value.</dd>


<dt>make.grid</dt>
<dd>a logical. If FALSE, a list is returned, otherwise
<code>fast.grid</code> is applied to the list before returning it.</dd>

</dl>

allGenotypes: Genotype combinations

Description

Usage

Value

Arguments

Examples