IHWpaper
This is the development version of IHWpaper; for the stable release version, see IHWpaper.
Reproduce figures in IHW paper
Bioconductor version: Development (3.24)
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("IHWpaper")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 |
Details
| biocViews | ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch |
| Version | 1.41.0 |
| 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 |
See More
| 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 | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IHWpaper_1.41.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |