swfdr

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

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

Bioconductor version: Development (3.24)

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")):

Jeffrey T. Leek, Leah Jager, Simina M. Boca, Tomasz Konopka. swfdr: Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates. doi:10.18129/B9.bioc.swfdr, R package version 1.39.0, https://bioconductor.org/packages/swfdr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MultipleComparison, Software, StatisticalMethod
Version	1.39.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 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

Suggests	dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	swfdr_1.39.0.tar.gz
Windows Binary (x86_64)	swfdr_1.39.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	swfdr_1.39.0.tgz
macOS Binary (sonoma-arm64)	swfdr_1.39.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/swfdr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/swfdr
Package Short Url	https://bioconductor.org/packages/swfdr/
Package Downloads Report	Download Stats