R Observatory: Metrics for CoxMK version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CoxMK

0.1.1

A Model-X Knockoff Method for Genome-Wide Survival Association Analysis

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yang ChenFirst published 2025-09-031 releasesCRAN page ↗

A genome-wide survival framework that integrates sequential conditional independent tuples and saddlepoint approximation method, to provide SNP-level false discovery rate control while improving power, particularly for biobank-scale survival analyses with low event rates. The method is based on model-X knockoffs as described in Barber and Candes (2015) doi:10.1214/15-AOS1337 and fast survival analysis methods from Bi et al. (2020) doi:10.1016/j.ajhg.2020.06.003. A shrinkage algorithmic leveraging accelerates multiple knockoffs generation in large genetic cohorts. This CRAN version uses standard Cox regression for association testing. For enhanced performance on very large datasets, users may optionally install the 'SPACox' package from GitHub which provides saddlepoint approximation methods for survival analysis.

Install

R (CRAN)Ubuntu (r2u)

install.packages("CoxMK", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-coxmk

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: 1.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2K

CRAN downloads in the past year

Rank #22,032 · ~5/day · ~166/mo

Releases R versions

Daily download trend is not available in this view yet.

13630 days

51190 days

2K1 year

Compare downloads with other packages →

Also on72 r2u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

Matrixsurvivalirlbastatsutilsgdsfmt BEDMatrix

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Yang Chen

Author, Maintainer

Authors (1)

Yang Chen

Author, Maintainer

Contributors (1)

Contributors

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-03
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 64 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CoxMK")

Format

Chen, Y., & Contributors. (2025). CoxMK: A Model-X Knockoff Method for Genome-Wide Survival Association Analysis (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.CoxMK

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 CoxMK version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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