splitGenotypes

Converts a matrix or data frame with one genotype column per marker into a matrix with
two allele columns per marker. Malformed genotypes give an error.

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

splitGenotypes function

<dl><dt>x</dt>
<dd>A matrix or data frame containing genotypes.</dd>
<dt>sep</dt>
<dd>Allele separator. If NULL, detected automatically from the first 50
non-missing genotypes, trying "/", ",", "-", ";" and " ".</dd>
<dt>missing</dt>
<dd>Symbol for missing alleles (default 0).</dd>
<dt>clean</dt>
<dd>If TRUE, trim whitespace and fill in missing individual alleles, e.g. "1/"
becomes "1/0". Default FALSE for speed.</dd>
<dt>colNames</dt>
<dd>If TRUE, append <code>.1</code> and <code>.2</code> to the input column names. If FALSE
(default), columns are unnamed.</dd></dl>

Arguments

Split genotype columns into allele columns — splitGenotypes

<dl>

<dt>x</dt>
<dd>A matrix or data frame containing genotypes.</dd>


<dt>sep</dt>
<dd>Allele separator. If NULL, detected automatically from the first 50
non-missing genotypes, trying "/", ",", "-", ";" and " ".</dd>


<dt>missing</dt>
<dd>Symbol for missing alleles (default 0).</dd>


<dt>clean</dt>
<dd>If TRUE, trim whitespace and fill in missing individual alleles, e.g. "1/"
becomes "1/0". Default FALSE for speed.</dd>


<dt>colNames</dt>
<dd>If TRUE, append <code>.1</code> and <code>.2</code> to the input column names. If FALSE
(default), columns are unnamed.</dd>

</dl>

splitGenotypes: Split genotype columns into allele columns

Description

Usage

Value

Arguments

Examples