CpGassoc

2.70

Association Between Methylation and a Phenotype of Interest

0packages depend

4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by R BarfieldFirst published 2012-05-2213 releasesCRAN page ↗

Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Install

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

install.packages("CpGassoc", 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-cpgassoc

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-CpGassoc

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-CpGassoc

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: 2.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 71%
References docs: 0%

Downloads

CRAN downloads in the past year

Rank #10,985 · ~11/day · ~329/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

97590 days

4K1 year

Compare downloads with other packages →

Also on144 r2u41 autocran1.4K conda_forge43 c2d4u

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (3)

R >= 2.10nlmemethods

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

R 2,404 (50%)Rd 1,408 (30%)Vignettes 952 (20%)

Code characteristics

Object systems

S317

Cyclomatic complexity: 5.0 median / 67 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

31 7 exported

Complexity

13.5 avg / 67 max

Call network

31 nodes / 23 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
annotation	data.frame	1,228 × 3	–
samplepheno	data.frame	258 × 6	–

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (6)

Barfield

no longer listed · 1.00 to 2.70

Conneely

no longer listed · 1.00 to 2.70

Kilaru

no longer listed · 1.00 to 2.70

Package Timeline

13 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
2.70Latest
2024-07-16 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
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
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
2.60
2017-05-31 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
2.55
2016-01-29 · diff ↗
R
R 3.2.0 released · 2015-04-16
2.50
2015-01-28 · diff ↗

Show 12 earlier events

R
R 3.1.0 released · 2014-04-10
2.11
2014-01-10 · diff ↗
3.0.3
2014-01-02 · diff ↗
3.0.2
2013-09-16 · diff ↗
2.0
2013-09-16 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.3
2012-07-18 · diff ↗
2.15.2
2012-07-17 · diff ↗
1.1
2012-05-26 · diff ↗
2.15.1
2012-05-25 · diff ↗
1.00
2012-05-22
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-05-22
Total releases: 13 / 14 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 1.4 MB / 4 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Mixed, Multilevel, and Hierarchical Models in R

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