This package was removed from CRAN on 2022-11-28. Its history is shown below.

Reason: the request of the maintainer

Details below reflect version 1.7.0, its last release before removal.

snpEnrichment

1.7.0

SNPs Enrichment Analysis

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Mickael Canouil10 releasesCRAN page ↗GitHub ↗

Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/snpEnrichment/snpEnrichment_1.7.0.tar.gz"
pkgFile <- "snpEnrichment_1.7.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.7.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

Development version from mcanouil/snpEnrichment. 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-snpenrichment

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

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.06

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMEYes · 101 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 53%
Documented parameters: 100%
Return-value docs: 100%
References docs: 10%

Downloads

snpEnrichment Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on77 r2u

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0.0methods

Imports (8)

parallelsnpStatsgridggplot2grDevicesgraphicsstatsutils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,819 (66%)Rd 1,428 (34%)

Code characteristics

Object systems

S4 class3S4 generic13S4 method34

Cyclomatic complexity: 3.0 median / 25 max
Test cases: 2 / 0.06 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

27 5 exported

Complexity

4.4 avg / 25 max

Call network

27 nodes / 36 edges

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

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
transcript	data.frame	950 × 2	–

People & History

People (2)

Maintainer (1)

Mickael Canouil

Author, Maintainer

Authors (1)

Mickael Canouil

Author, Maintainer

Contributors (1)

Loic Yengo

Contributor

Package Timeline

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

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-28
the request of the maintainer
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
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.7.0
2015-10-01 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.6.3
2015-01-15 · diff ↗
1.6.0
2014-11-04 · diff ↗
1.5-0
2014-09-26 · diff ↗
1.4-1
2014-09-11 · diff ↗
R
R 3.1.0 released · 2014-04-10

Show 6 earlier events

1.4-0
2014-01-27 · diff ↗
1.2-3
2013-09-27 · diff ↗
1.1-3
2013-07-25 · diff ↗
1.1-0
2013-05-22 · diff ↗
1.0-0
2013-04-25
R
R 3.0.0 released · 2013-04-03

Package metadata

Total releases: 10
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.0
Bundled data: 400 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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