README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  fig.align = "center",
  dpi = 300
)
```

# pedtools <img src="man/figures/logo.png" align="right" height=140/>

<!-- badges: start -->
[![CRAN status](https://www.r-pkg.org/badges/version/pedtools)](https://CRAN.R-project.org/package=pedtools)
[![](https://cranlogs.r-pkg.org/badges/grand-total/pedtools?color=yellow)](https://cran.r-project.org/package=pedtools)
[![](https://cranlogs.r-pkg.org/badges/last-month/pedtools?color=yellow)](https://cran.r-project.org/package=pedtools)
<!-- badges: end -->

## 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](https://CRAN.R-project.org/package=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](https://github.com/magnusdv/pedsuite) and a dedicated [website](https://magnusdv.github.io/pedsuite/) offering more information.

#### Citation
If you use **pedtools** in a publication, please cite the book [Pedigree Analysis in R](https://shop.elsevier.com/books/pedigree-analysis-in-r/vigeland/978-0-12-824430-2)
(Vigeland, 2021. Academic Press. ISBN:<span>9780128244302</span>).

#### Online app
Try the online app **QuickPed** for building and analysing pedigrees here: [https://magnusdv.shinyapps.io/quickped/](https://magnusdv.shinyapps.io/quickped/)


## Installation
To get **pedtools**, install from CRAN as follows:
```{r, eval = FALSE}
install.packages("pedtools")
```

Alternatively, fetch the latest development version from GitHub:
```{r, eval = FALSE}
devtools::install_github("magnusdv/pedtools")
```

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

```{r example, fig.height = 3, fig.width = 3.5, out.width = "40%", message = FALSE}
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:
```{r}
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](https://cran.r-project.org/package=pedtools/vignettes/pedtools.html) is a good place to start.