Package: sumFREGAT 1.2.5

Nadezhda M. Belonogova

sumFREGAT: Fast Region-Based Association Tests on Summary Statistics

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.

Authors:Nadezhda M. Belonogova <belon@bionet.nsc.ru> and Gulnara R. Svishcheva <gulsvi@bionet.nsc.ru> with contributions from: Seunggeun Lee, Pierre Lafaye de Micheaux, Thomas Lumley, Minghui Wang, Yiyuan Liu, Shizhong Han, Yaowu Liu, James O. Ramsay, Xihao Li, Zilin Li, and Han Chen

sumFREGAT_1.2.5.tar.gz
sumFREGAT_1.2.5.tar.gz(r-4.5-noble)sumFREGAT_1.2.5.tar.gz(r-4.4-noble)
sumFREGAT_1.2.5.tgz(r-4.4-emscripten)sumFREGAT_1.2.5.tgz(r-4.3-emscripten)
sumFREGAT.pdf |sumFREGAT.html✨
sumFREGAT/json (API)

# Install 'sumFREGAT' in R:
install.packages('sumFREGAT', repos = 'https://cloud.r-project.org')
Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

1.30 score 2 stars 278 downloads 1 mentions 12 exports 11 dependencies

Last updated 3 years agofrom:f0e227c90a. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-linux-x86_64OKMar 31 2025
R-4.4-linux-x86_64OKMar 31 2025

Exports:ACATACATOBTFLMminpPCAprep.score.filessimpleMSKATSKATOsumchisumSTAAR

Dependencies:BHGBJlatticeMatrixmvtnormRcppRcppEigenRSpectraseqminerSKATSPAtest

Citation

To cite package ‘sumFREGAT’ in publications use:

Belonogova NM, Lee GRSwcfS, de Micheaux PL, Lumley T, Wang M, Liu Y, Han S, Liu Y, Ramsay JO, Li X, Li Z, Chen H (2022). sumFREGAT: Fast Region-Based Association Tests on Summary Statistics. R package version 1.2.5, https://CRAN.R-project.org/package=sumFREGAT.

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.

Corresponding BibTeX entry: 

  @Manual{,
    title = {sumFREGAT: Fast Region-Based Association Tests on Summary
      Statistics},
    author = {Nadezhda M. Belonogova and Gulnara R. Svishcheva with
      contributions from: Seunggeun Lee and Pierre Lafaye {de Micheaux}
      and Thomas Lumley and Minghui Wang and Yiyuan Liu and Shizhong
      Han and Yaowu Liu and James O. Ramsay and Xihao Li and Zilin Li
      and Han Chen},
    year = {2022},
    note = {R package version 1.2.5},
    url = {https://CRAN.R-project.org/package=sumFREGAT},
  }