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

DOI: 10.18129/B9.bioc.IHWpaper

Reproduce figures in IHW paper

Bioconductor version: Release (3.5)

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 1.4.0
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
Build Report

Package Archives

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

Source Package IHWpaper_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/IHWpaper
Package Short Url http://bioconductor.org/packages/IHWpaper/
Package Downloads Report Download Stats

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