segregatr

0.5.0

Segregation Analysis for Variant Interpretation

1packages depend

2.9Kdownloads / year

71.9%test coverage

13/13checks pass

Overview

About

Maintained by Magnus Dehli VigelandFirst published 2021-04-154 releasesCRAN page ↗GitHub ↗

An implementation of the full-likelihood Bayes factor (FLB) for evaluating segregation evidence in clinical medical genetics. The method was introduced by Thompson et al. (2003) doi:10.1086/378100. This implementation supports custom penetrance values and liability classes, and allows visualisations and robustness analysis as presented in Ratajska et al. (2023) doi:10.1002/mgg3.2107. See also the online app 'shinyseg', https://chrcarrizosa.shinyapps.io/shinyseg, which offers interactive segregation analysis with many additional features (Carrizosa et al. (2024) doi:10.1093/bioinformatics/btae201).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("segregatr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("magnusdv/segregatr")

Development version from magnusdv/segregatr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-segregatr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-segregatr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-segregatr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.96

71.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 299 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 67%
References docs: 50%

Downloads

2.9K

CRAN downloads in the past year

Rank #15,237 · ~8/day · ~239/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

73690 days

2.9K1 year

Compare downloads with other packages →

Also on103 r2u13 autocran

Repository

GitHub ↗ magnusdv/segregatr

3Stars

1Forks

0Open issues

0Open PRs

4Releases

83Commits

2Contributors

medical-geneticspedigree-analysispedsuitesegregation-analysisvariant-interpretation

83 commits · Last activity 2025-08-27

Stars over time

2024-09-13 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/magnusdv/segregatr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0pedtools

Imports (1)

pedprobr

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

pedsuite

Code & Tests

Code Composition

R 1,639 (84%)Rd 304 (16%)

Code characteristics

Cyclomatic complexity: 8.0 median / 27 max
Test cases: 18 / 0.96 per code line

Test coverage

Line coverage

72%

Expression

71.9%

Tests / Examples

71.9% / 82% ex

Functions

15 3 exported

Complexity

9.1 avg / 27 max

Call network

15 nodes / 13 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

15 functions

Function	Cyclo	Coverage
sFLB exp	6	0%
.myintersect	1	0%
.mysetdiff	1	0%
isCount	5	0%
rareDistr	9	0%
plotSegregation exp	27	72%

People & History

People (2)

Maintainer (1)

Magnus Dehli Vigeland

Author, Maintainer

Authors (2)

Magnus Dehli Vigeland

Author, Maintainer

Christian Carrizosa

Author · added in 0.3.0

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
2025-08-27 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.4.0
2024-06-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.0
2023-06-26 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.0
2021-04-15
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-15
Total releases: 4 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 31 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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