Package: swfdr 1.33.0

Simina M. Boca

swfdr: Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates

This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ.

Authors:Jeffrey T. Leek, Leah Jager, Simina M. Boca, Tomasz Konopka

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swfdr.pdf |swfdr.html✨
swfdr/json (API)
NEWS

# Install 'swfdr' in R:
install.packages('swfdr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/leekgroup/swfdr/issues

Datasets:
  • BMI_GIANT_GWAS_sample - Subset of SNPs from meta-analysis of BMI GWAS study.
  • journals_pVals - P-values from abstracts from articles in 5 biomedical journals (American Journal of Epidemiology, BMJ, JAMA, Lancet, New England Journal of Medicine), over 11 years (2000-2010).

On BioConductor:swfdr-1.33.0(bioc 3.21)swfdr-1.32.0(bioc 3.20)

multiplecomparisonstatisticalmethodsoftware

6.25 score 3 stars 37 scripts 268 downloads 2 mentions 3 exports 0 dependencies

Last updated 5 months agofrom:fa8b787f82. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 07 2025
R-4.5-winWARNINGMar 07 2025
R-4.5-macWARNINGMar 07 2025
R-4.5-linuxWARNINGMar 07 2025
R-4.4-winWARNINGMar 07 2025
R-4.4-macWARNINGMar 07 2025
R-4.4-linuxWARNINGMar 07 2025
R-4.3-winWARNINGMar 07 2025
R-4.3-macWARNINGMar 07 2025

Exports:calculateSwfdrlm_pi0lm_qvalue

Dependencies:

Computing q-values conditioned on covariates using swfdr

Rendered fromswfdrQ.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2021-01-05
Started: 2019-04-22

Tutorial for swfdr package

Jeff Leek, Simina Boca

Rendered fromswfdrTutorial.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2019-04-22
Started: 2016-10-20