Package: swfdr 1.38.0

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

swfdr_1.38.0.tar.gz
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swfdr_1.38.0.tgz(r-4.6-any)swfdr_1.38.0.tgz(r-4.5-any)
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swfdr_1.38.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
swfdr/json (API)
NEWS

# Install 'swfdr' in R:
install.packages('swfdr', repos = c('https://bioc-release.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-1.39.0(bioc 3.24)swfdr-1.38.0(bioc 3.23)

multiplecomparisonstatisticalmethodsoftware

6.44 score 3 stars 58 scripts 426 downloads 2 mentions 3 exports 0 dependencies

Last updated from:33304cf0c2 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR177
linux-devel-x86_64WARNING188
source / vignettesOK180
linux-release-x86_64WARNING123
macos-release-arm64WARNING84
macos-oldrel-arm64WARNING76
windows-develWARNING86
windows-releaseWARNING67
windows-oldrelWARNING75
wasm-releaseOK97

Exports:calculateSwfdrlm_pi0lm_qvalue

Dependencies:

Computing q-values conditioned on covariates using swfdr

Rendered fromswfdrQ.Rmdusingknitr::rmarkdownon May 30 2026.

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

Tutorial for swfdr package

Jeff Leek, Simina Boca

Rendered fromswfdrTutorial.Rmdusingknitr::rmarkdownon May 30 2026.

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