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swfdr

This is the development version of swfdr; for the stable release version, see swfdr.

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


Bioconductor version: Development (3.19)

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.

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

Maintainer: Simina M. Boca <smb310 at georgetown.edu>, Jeffrey T. Leek <jtleek at gmail.com>

Citation (from within R, enter citation("swfdr")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("swfdr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("swfdr")
Computing covariate-adjusted q-values PDF R Script
Tutorial for swfdr package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews MultipleComparison, Software, StatisticalMethod
Version 1.29.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>= 3)
Depends R (>= 3.4)
Imports methods, splines, stats4, stats
System Requirements
URL https://github.com/leekgroup/swfdr
Bug Reports https://github.com/leekgroup/swfdr/issues
See More
Suggests dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package swfdr_1.29.0.tar.gz
Windows Binary swfdr_1.29.0.zip
macOS Binary (x86_64) swfdr_1.29.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/swfdr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/swfdr
Bioc Package Browser https://code.bioconductor.org/browse/swfdr/
Package Short Url https://bioconductor.org/packages/swfdr/
Package Downloads Report Download Stats