R Observatory: Metrics for KnockoffTrio version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

KnockoffTrio

1.1.0Package record

GWAS with Trio and Duo Data using Knockoff Statistics for FDR Control

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yi YangCRAN page ↗

Identification of putative causal variants in genome-wide association studies with trio and duo families. The package calculates the W feature statistics from KnockoffTrio and p-values from the family-based association test (FBAT) using trio and/or duo data. Compared to previous versions, a significant improvement has been made in Version 1.1.0 to allow the package to be applied not only to trio families but also to duo families. The package implements the methods in the paper: "Yang, Y., Wang, C., Liu, L., Buxbaum, J., He, Z., & Ionita-Laza, I. (2022). KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. The American Journal of Human Genetics, 109(10), 1761-1776."

Install

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

install.packages("KnockoffTrio", 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-knockofftrio

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-KnockoffTrio

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-KnockoffTrio

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: 48 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #21,067 · ~9/day · ~287/mo

Releases R versions

Daily download trend is not available in this view yet.

25030 days

63590 days

3.4K1 year

Compare downloads with other packages →

Also on70 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing KnockoffTrio adds no packages beyond those that come with R.

Depends (1)

R >= 2.10

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Yi Yang

Author, Maintainer since 1.0.0 (2022)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.0Latest
record
2025-01-23 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.2
record
2023-12-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
record
2022-10-17 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-03-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-07
Total releases: 4 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 0.3 KB / 1 file
Download size: 15 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("KnockoffTrio")

Format

Yang, Y. (2025). KnockoffTrio: GWAS with Trio and Duo Data using Knockoff Statistics for FDR Control (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.KnockoffTrio

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 KnockoffTrio version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →