validatePed

Validate the internal pedigree structure. The input may be either a (possibly
malformed) <code>ped()</code> object, or its defining vectors <code>id</code>, <code>fid</code>, <code>mid</code>, <code>sex</code>.

A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).

Magnus Vigeland

pedtools

Creating and Working with Pedigrees and Marker Data

Magnus Dehli Vigeland

validatePed function

<dl><dt>x</dt>
<dd>A <code>ped</code> object.</dd>
<dt>id</dt>
<dd>A vector (numeric or character) of individual ID labels.</dd>
<dt>fid</dt>
<dd>A vector of the same length as <code>id</code>, containing the labels of the
fathers. In other words <code>fid[i]</code> is the father of <code>id[i]</code>, or 0 if <code>id[i]</code>
is a founder.</dd>
<dt>mid</dt>
<dd>A vector of the same length as <code>id</code>, containing the labels of the
mothers. In other words <code>mid[i]</code> is the mother of <code>id[i]</code>, or 0 if <code>id[i]</code>
is a founder.</dd>
<dt>sex</dt>
<dd>A numeric of the same length as <code>id</code>, describing the genders of
the individuals (in the same order as <code>id</code>.) Each entry must be either 1
(=male), 2 (=female) or 0 (=unknown).</dd></dl>

Arguments

Pedigree errors — validatePed

<dl>

<dt>x</dt>
<dd>A <code>ped</code> object.</dd>


<dt>id</dt>
<dd>A vector (numeric or character) of individual ID labels.</dd>


<dt>fid</dt>
<dd>A vector of the same length as <code>id</code>, containing the labels of the
fathers. In other words <code>fid[i]</code> is the father of <code>id[i]</code>, or 0 if <code>id[i]</code>
is a founder.</dd>


<dt>mid</dt>
<dd>A vector of the same length as <code>id</code>, containing the labels of the
mothers. In other words <code>mid[i]</code> is the mother of <code>id[i]</code>, or 0 if <code>id[i]</code>
is a founder.</dd>


<dt>sex</dt>
<dd>A numeric of the same length as <code>id</code>, describing the genders of
the individuals (in the same order as <code>id</code>.) Each entry must be either 1
(=male), 2 (=female) or 0 (=unknown).</dd>

</dl>

validatePed: Pedigree errors

Description

Usage

Value

Arguments

Examples