snplinkage

1.2.0

Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

0packages depend

2.8Kdownloads / year

–test coverage

1/13checks pass

Overview

About

Maintained by Thomas CharlonFirst published 2023-05-042 releasesCRAN page ↗GitLab ↗

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) doi:10.13097/archive-ouverte/unige:161795.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("snplinkage", 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("thomaschln/snplinkage")

Development version from thomaschln/snplinkage. 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-snplinkage

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

Health

CRAN checks

12NOTE1OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 14.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.12

not tracked

Coverage

90%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-27
1 OK · 12 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
1 OK · 11 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
1 OK · 12 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
1 OK · 11 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
1 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 100%
References docs: 0%

Downloads

2.8K

CRAN downloads in the past year

Rank #17,634 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

19830 days

66490 days

2.8K1 year

Compare downloads with other packages →

Also on170 r2u

Repository

GitLab ↗ thomaschln/snplinkage

Repository practices

Upstream repositoryBeta

Repository gitlab.com/thomaschln/snplinkage is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.15GWASTools

Imports (17)

biomaRt cowplot data.table gdsfmt ggplot2 ggrepelgridgrDevicesgtable knitr magrittrmethodsparallelreshape2 SNPRelatestatsutils

LinkingTo (0)

none

Suggests (2)

rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,910 (58%)Rd 1,541 (31%)Vignettes 480 (10%)Other 80 (2%)

Code characteristics

Object systems

S322S4 class1S4 method9

Cyclomatic complexity: 2.0 median / 17 max
Test cases: 12 / 0.12 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

106 27 exported

Complexity

2.5 avg / 17 max

Call network

106 nodes / 105 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
crohn	data.frame	387 × 212	in 3 packages

People & History

People (4)

Maintainer (1)

Thomas Charlon

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

2 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
1.2.0Latest
2024-09-09 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.0
2023-05-04
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-04
Total releases: 2 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.15
Bundled data: 16 KB / 1 file
Download size: 4.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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