skewr
This is the development version of skewr; for the stable release version, see skewr.
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Bioconductor version: Development (3.24)
The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.
Author: Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]
Maintainer: Ryan Putney <ryanputney at gmail.com>
citation("skewr")):
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("skewr")
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("skewr")| An Introduction to the skewr Package | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.45.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest |
| Imports | minfi, S4Vectors(>= 0.19.1), RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | GEOquery, knitr, minfiData |
| Linking To | |
| 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 | skewr_1.45.0.tar.gz |
| Windows Binary (x86_64) | skewr_1.45.0.zip |
| macOS Binary (big-sur-x86_64) | skewr_1.45.0.tgz |
| macOS Binary (sonoma-arm64) | skewr_1.45.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/skewr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/skewr |
| Bioc Package Browser | https://code.bioconductor.org/browse/skewr/ |
| Package Short Url | https://bioconductor.org/packages/skewr/ |
| Package Downloads Report | Download Stats |