swfdr

DOI: 10.18129/B9.bioc.swfdr    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see swfdr.

Science-wise false discovery rate and proportion of true null hypotheses estimation

Bioconductor version: 3.10

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 proportion of true null hypotheses in the presence of 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>

Installation

To install this package, start R (version "3.6") and enter:

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

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")

 

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

Details

biocViews	MultipleComparison, Software, StatisticalMethod
Version	1.12.0
In Bioconductor since	BioC 3.5 (R-3.4) (3 years)
License	GPL (>= 3)
Depends	R (>= 3.4)
Imports	splines, stats4, stats
LinkingTo
Suggests	dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	swfdr_1.12.0.tar.gz
Windows Binary	swfdr_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	swfdr_1.12.0.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