IHW

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

Independent Hypothesis Weighting

Bioconductor version: Development (3.24)

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

Author: Nikos Ignatiadis [aut, cre], Wolfgang Huber [aut]

Maintainer: Nikos Ignatiadis <nikos.ignatiadis01 at gmail.com>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

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("IHW")

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("IHW")

Introduction to IHW	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MultipleComparison, RNASeq, Software
Version	1.41.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	Artistic-2.0
Depends	R (>= 3.3.0)
Imports	methods, slam, lpsymphony, fdrtool, BiocGenerics
System Requirements
URL

Suggests	ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools
Linking To
Enhances
Depends On Me	IHWpaper
Imports Me	ideal, scp
Suggests Me	DEWSeq, GRaNIE, metagenomeSeq, muscat, DGEobj.utils, readyomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	IHW_1.41.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	IHW_1.41.0.tgz
macOS Binary (sonoma-arm64)	IHW_1.41.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IHW
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IHW
Bioc Package Browser	https://code.bioconductor.org/browse/IHW/
Package Short Url	https://bioconductor.org/packages/IHW/
Package Downloads Report	Download Stats