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pedtools

Creating and Working with Pedigrees and Marker Data

A lightweight, but 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. Pedigree plots are produced by wrapping the plotting functionality of the 'kinship2' package.

Functions (44)

as.data.frame.ped

Convert ped to data.frame

as.matrix.ped

Convert ped to matrix

Conversions to ped objects

connectedComponents

Connected pedigree components

Family identifier

founderInbreeding

Inbreeding coefficients of founders

freqDatabase

Allele frequency database

Allele matrix manipulation

getComponent

Pedigree component

getGenotypes

Genotype matrix

Tabulate marker positions

Get or set the sex of pedigree members

inbreedingLoops

Pedigree loops

Test if something is a marker

Is an object a ped object?

locusAttributes

Get or set locus attributes

Marker objects

marker_attach

Attach markers to pedigrees

marker_getset

Get/set marker attributes

marker_prop

Marker properties

marker_select

Select or remove attached markers

mendelianCheck

Check for Mendelian errors

Merge two pedigrees

The number of markers attached to a pedigree

Internal ped constructor

ped

Pedigree construction

Create simple pedigrees

ped_complex

Complex pedigree structures

ped_internal

Internal ordering of pedigree members

Add/remove pedigree members

ped_subgroups

Pedigree subgroups

Pedigree utilities

pedtools: Tools for working with pedigrees in R

Plot pedigrees with genotypes

plotPedList

Plot a collection of pedigrees.

print.nucleus

S3 methods

Printing pedigrees

Random pedigree

Read a pedigree from file

Get or modify pedigree labels

sortGenotypes

Sort the alleles in each genotype

transferMarkers

Transfer marker data

validatePed

Pedigree errors

Write a pedigree to file

pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)

Initial release

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