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 a continuation of the paramlink package, which is no longer actively developed.

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

We create a pedigree with a consanguineous mating between half siblings. The child has genotype A/B at a SNP marker.

library(pedtools)

x = halfSibPed(sex1 = 1, sex2 = 2)
x = addChildren(x, father = 4, mother = 5, nch = 1)

m = marker(x, "6" = c("A", "B"))
plot(x, m, skip.empty.genotypes = TRUE)

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