R Observatory: Metrics for sumFREGAT version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2026-01-29. Its history is shown below.

Reason: requires archived package 'seqminer'

Details below reflect version 1.2.5, its last release before removal.

sumFREGAT

1.2.5Package record

Fast Region-Based Association Tests on Summary Statistics

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Nadezhda M. BelonogovaCRAN page ↗

An adaptation of classical region/gene-based association analysis techniques to the use of summary statistics (P values and effect sizes) and correlations between genetic variants as input. It is a tool to perform the most popular and efficient gene-based tests using the results of genome-wide association (meta-)analyses without having the original genotypes and phenotypes at hand. See for details: Svishcheva et al (2019) Gene-based association tests using GWAS summary statistics. Bioinformatics. Belonogova et al (2022) SumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics. PLOS Comp Biol.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/sumFREGAT/sumFREGAT_1.2.5.tar.gz"
pkgFile <- "sumFREGAT_1.2.5.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 (1.2.5) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.5

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5includes a package overview page
Examples that run: 75%3 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 60%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on340 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (5)

methodsMatrixsplinesseqminer GBJ

LinkingTo (0)

none

Suggests (1)

data.table

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (12)

Nadezhda M. Belonogova

Contributor

Gulnara R. Svishcheva with contributions from: Seunggeun Lee

Contributor

Pierre Lafaye de Micheaux

Contributor

Thomas Lumley

Contributor

Minghui Wang

Contributor · added in 1.1.0

Yiyuan Liu

Contributor · added in 1.1.0

Shizhong Han

Contributor · added in 1.2.0

Yaowu Liu

Contributor · added in 1.2.0

Show 4 more peopleHide 4 people

James O. Ramsay

Contributor

Xihao Li

Contributor · added in 1.2.3

Zilin Li

Contributor · added in 1.2.3

Han Chen

Contributor · added in 1.2.3

Maintainer since 1.0.0 (2018)

Listed in earlier versions (1)

Shizhong Han Thomas Lumley

no longer listed · 1.1.0

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-01-29
requires archived package 'seqminer'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.5
record
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.4
record
2022-03-24 · diff ↗
1.2.3
record
2022-03-09 · diff ↗
1.2.2
record
2021-10-19 · diff ↗ ·
removed 2 exports
FFGAS, MLR
R
R 4.1.0 released · 2021-05-18
1.2.1
record
2021-02-28 · diff ↗ ·
added 1 export
FFGAS
1.2.0
record
2020-12-16 · diff ↗ ·
added 3 exports
ACAT, ACATO, sumSTAAR
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1.0
record
2018-11-15 · diff ↗ ·
added 4 exports
simpleM, minp, SKATO, sumchi

Show 3 earlier eventsHide 3 earlier events

R
R 3.5.0 released · 2018-04-23
1.0.0
record
2018-01-17
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-01-17
Total releases: 8 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sumFREGAT")

Format

Belonogova, N. M., Lee, G. R. S. w. c. f. S., Micheaux, P. L. d., Lumley, T., Wang, M., Liu, Y., Han, S., Liu, Y., Ramsay, J. O., Li, X., Li, Z., & Chen, H. (n.d.). sumFREGAT: Fast Region-Based Association Tests on Summary Statistics (Version 1.2.5) [Computer software]. Retrieved October 27, 2026, from https://CRAN.R-project.org/package=sumFREGAT

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 sumFREGAT version 1.2.5 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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