R Observatory: Metrics for GWASTools version 1.58.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GWASTools

Bioc current

Tools for Genome Wide Association Studies

v1.58.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.9 · Nov 1, 2011

Current · Requires R 4.6

1.0 In 30 of 49 releases 3.23

Description

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

192 93 exported

Complexity

9.8 avg / 89 max

Call network

192 nodes / 192 edges

Test coverage is not measured for Bioconductor packages; 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.

Code

Structure

Lines of code

27,855

Files

240

Compiled share

0%

Has compiled src

No

Language breakdown

R 15,897 (57.1%)Tests 4 (0%)Docs 8,730 (31.3%)Vignettes 3,224 (11.6%)

API

Exported functions

93

Internal functions

101

Recent export changes

v3.8+2 GenotypeIterator, GenotypeBlockIterator

v3.6+1 genoDataAsVCF

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

12.5%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

30

First release

2011-10-31

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

13

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 46 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 99%
Documented parameters: 99%
Return-value docs: 56%
References docs: 19%

Topics

Software › AssayDomain › SNP

Software › AssayDomain › GeneticVariability

Software › WorkflowStep › QualityControl

Software › Technology › Microarray

Depended on by (6)

Bioconductor (5)

GENESIS gwasurvivr mBPCR podkat GWASdata

CRAN (1)

snplinkage

People

At a glance

Version: 1.58.0
Category: software
License: Artistic-2.0
Requires R: ≥ 4.6
Maintainer: Stephanie M. Gogarten
Entered: 2.9 · Nov 1, 2011
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

BiobaseBioc

Imports

graphicsstatsutilsmethodsgdsfmt DBI RSQLite GWASExactHWDNAcopyBiocsurvival sandwich lmtest logistfquantsmoothBiocdata.table

Suggests

ncdf4GWASdataBiocBiocGenericsBiocRUnitBiostringsBiocGenomicRangesBiocIRangesBiocSNPRelatesnpStatsBiocS4VectorsBiocVariantAnnotationBiocparallelBiocStyleBiocknitr

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GWASTools")

Format

Gogarten, S. M., Bhangale, T., Conomos, M. P., Gogarten, S. M., Kumari, S., Laurie, C., Laurie, C., Lawrence, M., Levine, D., McHugh, C., Nelson, S., Painter, I., Shen, J., Stilp, A., Swarnkar, R., & Zheng, X. (2026). GWASTools: Tools for Genome Wide Association Studies (Version 1.58.0) [Computer software]. https://bioconductor.org/packages/GWASTools

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 GWASTools version 1.58.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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