To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IHWpaper")

In most cases, you don't need to download the package archive at all.

IHWpaper

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see IHWpaper.

Reproduce figures in IHW paper

Bioconductor version: 3.3

This package conveniently wraps all functions needed to reproduce the figures in the IHW preprint, available on biorXiv under http://biorxiv.org/content/early/2016/03/30/034330. Thus it is a companion package to the Bioconductor IHW package.

Author: Nikos Ignatiadis [aut, cre]

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IHWpaper")

Documentation

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

Details

biocViews	ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version	1.0.2
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, pasilla, DESeq, locfdr, tidyr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	IHWpaper_1.0.2.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Package Short Url	http://bioconductor.org/packages/IHWpaper/
Package Downloads Report	Download Stats

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