Creating and Working with Pedigrees and Marker Data.

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 feature imports machinery from the kinship2 package.

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

Citation

If you use pedtools in a publication, please cite the book Pedigree Analysis in R (Vigeland, 2021. Academic Press. ISBN:9780128244302).

Online app

Try the online app QuickPed for building and analysing pedigrees here: https://magnusdv.shinyapps.io/quickped/

Installation

To get pedtools, install from CRAN as follows:

install.packages("pedtools")

Alternatively, fetch the latest development version from GitHub:

devtools::install_github("magnusdv/pedtools")

Example

The following example illustrates a step-by-step creation of a pedigree with a marker object.

library(pedtools)

# Start with two half brothers
x = halfSibPed(type = "paternal")

# Make 5 female
x = swapSex(x, 5)

# Add a sister to 5 (parents are 2 and 3)
x = addDaughter(x, parents = 2:3)

# Add inbred child
x = addSon(x, parents = 4:5)

# Create marker
x = addMarker(x, "7" = "a/b")

# Plot pedigree with genotypes
plot(x, marker = 1, hatched = 7)

The process of building pedigrees is perfectly suited for the pipe operator |> recently introduced in R. For example, the above pedigree could have been created as follows:

x = halfSibPed(type = "paternal") |>
  swapSex(5) |>
  addDaughter(parents = 2:3) |>
  addSon(parents = 4:5) |>
  addMarker("7" = "a/b")

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