IHWpaper

DOI: 10.18129/B9.bioc.IHWpaper    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IHWpaper.

Reproduce figures in IHW paper

Bioconductor version: 3.7

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>

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IHWpaper")

 

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	1.7.0
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, pasilla, DESeq, locfdr, tidyr
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_1.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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	http://bioconductor.org/packages/IHWpaper/
Package Downloads Report	Download Stats