thgenetics

0.4-2

Genetic Rare Variants Tests

0packages depend

1.9Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Thomas HoffmannFirst published 2010-09-237 releasesCRAN page ↗

A step-up test for genetic rare variants in a gene or in a pathway. The method determines an optimal grouping of rare variants analytically. The method has been described in Hoffmann TJ, Marini NJ, and Witte JS (2010) doi:10.1371/journal.pone.0013584.

Install

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

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

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

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-thgenetics

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-thgenetics

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-thgenetics

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 45 s · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

1.9K

CRAN downloads in the past year

Rank #23,281 · ~5/day · ~158/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

48390 days

1.9K1 year

Compare downloads with other packages →

Also on412 r2u6 autocran

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

C++ 752 (72%)R 122 (12%)Rd 99 (9%)C 76 (7%)

Code characteristics

Cyclomatic complexity: 4.0 median / 7 max
Documented parameters: 91%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

27 2 exported

Complexity

4.6 avg / 7 max

Call network

27 nodes / 21 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (0)

Author records are not tracked yet for this package.

Release timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.4-2Latest
2018-04-18 · current release · diff ↗
0.4-0
2018-04-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.3-4.1
2016-07-10 · diff ↗
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10

Show 10 earlier events

R
R 3.0.0 released · 2013-04-03
0.3-4
2013-03-30 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.3-2
2011-09-28 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.3-1
2011-01-14 · diff ↗
R
R 2.12.0 released · 2010-10-15
0.3-0
2010-09-23
R
R 2.11.0 released · 2010-04-22

Package metadata

First published: 2010-09-23
Total releases: 7 / 16 yrs
License: GPL
Download size: 11 KB
Installed size: not tracked yet
With dependencies: not tracked yet