Registration and Call for Abstracts Open for Bioc2024

Pedixplorer

This is the development version of Pedixplorer; to use it, please install the devel version of Bioconductor.

Pedigree Functions


Bioconductor version: Development (3.19)

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Author: Louis Le Nézet [aut, cre] , Jason Sinnwell [aut], Terry Therneau [aut], Daniel Schaid [ctb], Elizabeth Atkinson [ctb], Louis Le Nezet [ctb]

Maintainer: Louis Le Nézet <louislenezet at gmail.com>

Citation (from within R, enter citation("Pedixplorer")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Pedixplorer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Pedixplorer")
Pedigree alignment details HTML R Script
Pedigree kinship() details HTML R Script
Pedigree object HTML R Script
Pedigree plotting details HTML R Script
Pedixplorer tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, DataRepresentation, Genetics, Software
Version 0.99.7
In Bioconductor since BioC 3.19 (R-4.4)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, testthat
System Requirements
URL https://github.com/LouisLeNezet/Pedixplorer
Bug Reports https://github.com/LouisLeLezet/Pedixplorer/issues
See More
Suggests diffviewer, vdiffr, rmarkdown, BiocStyle, knitr, withr, magick
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Pedixplorer_0.99.7.tar.gz
Windows Binary Pedixplorer_0.99.7.zip
macOS Binary (x86_64) Pedixplorer_0.99.7.tgz
macOS Binary (arm64) Pedixplorer_0.99.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/Pedixplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Pedixplorer
Bioc Package Browser https://code.bioconductor.org/browse/Pedixplorer/
Package Short Url https://bioconductor.org/packages/Pedixplorer/
Package Downloads Report Download Stats