IHWpaper

DOI: 10.18129/B9.bioc.IHWpaper    

Reproduce figures in IHW paper

Bioconductor version: Release (3.15)

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.

Author: Nikos Ignatiadis [aut, cre]

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("IHWpaper")

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("IHWpaper")

 

HTML	R Script	NMeth paper: Explaining tdr
HTML	R Script	NMeth paper: IHW-Bonferroni simulations
HTML	R Script	NMeth paper: Real data examples
HTML	R Script	NMeth paper: Simulation Figures
HTML	R Script	NMeth paper: Stratified Histograms
HTML	R Script	Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli
HTML	R Script	Various: BH explanation / visualization
HTML	R Script	Various: Grenander Estimator as applied to IHW (vs ECDF)
HTML	R Script	Various: Real data examples: 1-fold weight function
HTML	R Script	Various: tdr and pvalue rejection regions
HTML	R Script	Various: Weights vs Independent Filtering
PDF		Reference Manual

Details

biocViews	ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version	1.24.0
License	Artistic-2.0
Depends	R (>= 3.3), IHW
Imports	Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
LinkingTo	Rcpp
Suggests	testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
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	IHWpaper_1.24.0.tar.gz
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/IHWpaper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IHWpaper
Package Short Url	https://bioconductor.org/packages/IHWpaper/
Package Downloads Report	Download Stats