pedtools

Introduction

The goal of pedtools is to provide a lightweight, but comprehensive tool set for creating, manipulating and visualizing pedigrees with or without marker data. Common pedigree structures are quickly produced with tailor-made functions, while a range of utilities enable modifications like adding or removing individuals, extracting subsets, loop breaking, and merging pedigrees. The plotting functionality is imported from the kinship2 package.

pedtools is the hub of the ped suite, a collection of R packages for pedigree analysis, including applications in forensic and medical genetics. The ped suite has its own GitHub repository and a dedicated website offering more information.

Installation

To get pedtools, install from CRAN as follows:

install.packages("pedtools")

Alternatively, you can obtain the latest development version from GitHub:

# install.packages("devtools") # install devtools if needed
devtools::install_github("magnusdv/pedtools")

Example

The following example illustrates how pedigrees and markers may be built from scratch.

library(pedtools)

# Create pedigree
x = cousinPed(degree = 0, removal = 2)
x = addChildren(x, father = 3, nch = 2, sex = 2)

# Relabel according to plot order
x = relabel(x, "asPlot")

# Create marker and attach to pedigree
m = marker(x, "7" = "a/b", "11" = "b/b")

# Plot pedigree with genotypes
plot(x, marker = m, hatched = leaves(x))

For details about what pedtools can do, and many other examples, the vignette is the recommended place to start.