R Observatory: Metrics for sffdr version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sffdr

1.1.2

Surrogate Functional False Discovery Rates for Genome-Wide Association Studies

0packages depend

2.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Andrew BassFirst published 2024-12-023 releasesCRAN page ↗GitHub ↗

Pleiotropy-informed significance analysis of genome-wide association studies with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and $q$-value, and uses these estimates to derive a functional $p$-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization).

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("sffdr", 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("ajbass/sffdr")

Development version from ajbass/sffdr. 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-sffdr

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

13OK

Slowest check: 3.9 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.65

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 836 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 95%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #20,062 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

14630 days

55090 days

2.4K1 year

Compare downloads with other packages →

Also on422 r2u

Repository

GitHub ↗ ajbass/sffdr

5Stars

4Forks

0Open issues

0Open PRs

3Releases

73Commits

3Contributors

73 commits · Last activity 2026-04-01 · 0% stars, 30d

Stars over time

2025-03-06 · 42026-07-21 · 5

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ajbass/sffdr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (8)

locfitsplinesggplot2 patchwork qvalue fastglm withr Rcpp

LinkingTo (1)

Rcpp

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Andrew Bass

Author, Maintainer

Authors (2)

Andrew Bass

Author, Maintainer

Chris Wallace

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.2Latest
2026-03-31 · current release · diff ↗
1.1.0
2026-02-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-12-02
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-12-02
Total releases: 3 / 2 yrs
License: LGPL
Minimum R: ≥ 4.1.0
Bundled data: 252 KB / 1 file
Download size: 385 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sffdr")

Format

Bass, A., & Wallace, C. (2026). sffdr: Surrogate Functional False Discovery Rates for Genome-Wide Association Studies (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.sffdr

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 sffdr version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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