R Observatory: Metrics for SNPassoc version 2.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SNPassoc

2.3.1Package record

SNPs-Based Whole Genome Association Studies

0packages dependsuggested by 1

15.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Dolors PelegriCRAN page ↗GitHub ↗

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>. This version includes internal copies of functions from the archived 'haplo.stats' package to maintain functionality.

Install

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

install.packages("SNPassoc", 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("isglobal-brge/SNPassoc")

Development version from isglobal-brge/SNPassoc. 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-snpassoc

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-SNPassoc

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-SNPassoc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.1

READMEYes · 79 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 51 (2 internal)
Examples that run: 88%37 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 4 hold no code
Exported functions with examples: 85%
Documented parameters: 96%
Return-value docs: 95%
Help pages citing references: 25%

Vignettes (1)

SNPassoc: an R package to perform whole genome association studies

How these are measured

Downloads

15.5K

CRAN downloads in the past year

Rank #3,824 · ~42/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

98830 days

2.5K90 days

15.5K1 year

Compare downloads with other packages →

Also on268 r2u4 autocran2.1K conda_forge192 bioconda163 c2d4u

How downloads are counted

Repository

isglobal-brge/snpassoc ↗Account: isglobal-brge

16Stars

6Forks

3Open issues

0Open PRs

1Releases

80Commits

3Commit identities

80 commits · Last activity 2026-04-13 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-12-17 · 162026-07-07 · 16

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/isglobal-brge/snpassoc on 2026-10-21.

Continuous integration (1)

GitHub Actions

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing SNPassoc adds 73 packages (41 with compiled code, 71 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.0.0

Imports (9)

mvtnormparallelsurvivaltidyr plyr ggplot2 poisbinom rmsmethods

LinkingTo (0)

none

Suggests (10)

testthat knitr rmarkdown biomaRt VariantAnnotation GenomicRanges IRanges S4Vectors org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

gaawr2

How these are counted

Code & Tests

Datasets

People & History

People (3)

Dolors Pelegri

Author, Maintainer since 2.0-12 (2022) · added in 2.0-12

Juan R Gonzalez

Author

Victor Moreno

Author

Previously maintained by Juan R Gonzalez (2.0-0 to 2.0-11).

Releases (58)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-13
2.3.1Latest
record
2026-04-13 · current release · diff ↗ ·
added 12 exports
na.geno.keep, Ginv, haplo.em, haplo.glm, haplo.glm.control, haplo.model.frame, haplo.score, haplo.score.slide, louis.info, printBanner, setupGeno, score.sim.control
archivedRemoved from CRAN
2026-03-15
requires archived package 'haplo.stats'
R
R 4.5.0 released · 2025-04-11
2.1-2
record
2024-10-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.1-0
record
2022-12-14 · diff ↗ ·
removed 2 exports
dscore, pscore
2.0-18
record
2022-11-15 · diff ↗
unarchivedReturned to CRAN
2022-10-04
2.0-17
record
2022-10-04 · diff ↗
archivedRemoved from CRAN
2022-09-04
issues were not corrected in time
2.0-12
record
2022-08-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-12-03

Show 78 earlier eventsHide 78 earlier events

2.0-11
record
2021-12-03 · diff ↗ ·
added 7 exports
pscore, getNiceTable, getGeneSymbol, Table.N.Per, Table.mean.se, is.Monomorphic, sortSNPs
archivedRemoved from CRAN
2021-11-08
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
2.0-2
record
2020-11-11 · diff ↗
2.0-1
record
2020-10-13 · diff ↗
unarchivedReturned to CRAN
2020-09-07
2.0-0
record
2020-09-07 · diff ↗ ·
added 2 exports
related, dscore
archivedRemoved from CRAN
2020-08-27
requires archived package 'haplo.stats'
1.9-2.1
record
2020-08-19 · diff ↗
orphanedOrphaned by its maintainer
2020-08-17
email to maintainer is undeliverable
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
R
R 3.2.0 released · 2015-04-16
1.9-2
record
2014-04-23 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.9-1
record
2013-11-08 · diff ↗ ·
removed 1 export
dscore
1.9-1-dup
record
2013-11-08 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.8-5
record
2012-12-17 · diff ↗
1.8-5-dup
record
2012-09-03 · diff ↗
1.8-4
record
2012-09-03 · diff ↗
1.8-4-dup
record
2012-09-03 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.8-1
record
2011-11-22 · diff ↗ ·
added 1 export
dscore
R
R 2.14.0 released · 2011-10-31
1.8-1-dup
record
2011-09-14 · diff ↗
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
R
R 2.10.0 released · 2009-10-26
1.6-0
record
2009-07-18 · diff ↗
1.6-0-dup
record
2009-07-17 · diff ↗
R
R 2.9.0 released · 2009-04-17
1.5-8
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2009-03-09 · diff ↗
1.5-8-dup
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2009-03-09 · diff ↗
1.5-7
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2009-03-04 · diff ↗
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2009-03-04 · diff ↗
1.5-6
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2009-02-06 · diff ↗
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2009-02-06 · diff ↗
R
R 2.8.0 released · 2008-10-20
1.5-3
record
2008-05-05 · diff ↗
1.5-3-dup
record
2008-04-29 · diff ↗
1.5-2
record
2008-04-22 · diff ↗ ·
added 3 exports
LD, LDplot, LDtable
1.5-2-dup
record
2008-04-22 · diff ↗
R
R 2.7.0 released · 2008-04-22
1.5-1
record
2008-03-27 · diff ↗
1.5-1-dup
record
2008-03-27 · diff ↗
1.4-9
record
2007-10-16 · diff ↗
1.4-9-dup
record
2007-10-16 · diff ↗
R
R 2.6.0 released · 2007-10-03
1.4-8
record
2007-05-29 · diff ↗ ·
added 4 exports
odds, qqpval, GenomicControl, maxstat
1.4-8-dup
record
2007-05-23 · diff ↗
R
R 2.5.0 released · 2007-04-24
1.4-6
record
2007-03-23 · diff ↗
1.4-6-dup
record
2007-03-22 · diff ↗
1.4-5
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2007-03-21 · diff ↗
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2007-03-20 · diff ↗
1.4-4
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2007-03-20 · diff ↗
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2007-03-02 · diff ↗
1.4-3
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2007-01-22 · diff ↗
1.4-3-dup
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2007-01-19 · diff ↗
1.4-2
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2007-01-21 · diff ↗
1.4-2-dup
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2007-01-19 · diff ↗
1.4-1
record
2007-01-18 · diff ↗ ·
added 1 export
permTest
1.4-1-dup
record
2007-01-12 · diff ↗
1.3-0
record
2006-11-30 · diff ↗ ·
added 1 export
pvalues
1.3-0-dup
record
2006-11-29 · diff ↗
1.1-1
record
2006-11-19 · diff ↗ ·
added 1 export
scanWGassociation
1.1-1-dup
record
2006-11-14 · diff ↗
1.1-0
record
2006-11-10 · diff ↗ ·
added 19 exports
association, setupSNP, snp, WGassociation, intervals, plotMissing, getSignificantSNPs, tableHWE, Bonferroni.sig, haplo.interaction, interactionPval, additive, codominant, dominant, overdominant, recessive, int, make.geno, WGstats
1.1-0-dup
record
2006-11-09 · diff ↗
R
R 2.4.0 released · 2006-10-03
1.0-2
record
2006-09-29 · diff ↗
1.0-2-dup
record
2006-09-21
R
R 2.3.0 released · 2006-04-24

Package metadata

First published: 2006-09-21
Total releases: 58 / 20 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 770 KB / 8 files
Download size: 1.0 MB

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SNPassoc")

Format

Pelegri, D., Gonzalez, J. R., & Moreno, V. (2026). SNPassoc: SNPs-Based Whole Genome Association Studies (Version 2.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SNPassoc

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SNPassoc version 2.3.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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