IHWpaper

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see IHWpaper.

Reproduce figures in IHW paper

Bioconductor version: 3.14

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>

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

Installation

To install this package, start R (version "4.1") 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")

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 HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch

Version 1.22.0

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

System Requirements

URL

Suggests testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp

Linking To Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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Package Archives

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

Source Package IHWpaper_1.22.0.tar.gz

Windows Binary

macOS 10.13 (High Sierra)

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/

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