SNPchip

DOI: 10.18129/B9.bioc.SNPchip    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SNPchip.

Visualizations for copy number alterations

Bioconductor version: 3.10

Functions for plotting SNP array data; maintained for historical reasons

Author: Robert Scharpf <rscharpf at jhu.edu> and Ingo Ruczinski

Maintainer: Robert Scharpf <rscharpf at jhu.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SNPchip")

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("SNPchip")

 

PDF	R Script	Plotting Idiograms
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, GeneticVariability, SNP, Software, Visualization
Version	2.32.0
In Bioconductor since	BioC 2.0 (R-2.5) (13 years)
License	LGPL (>= 2)
Depends	R (>= 2.14.0)
Imports	methods, graphics, lattice, grid, foreach, utils, Biobase, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, oligoClasses(>= 1.31.1)
LinkingTo
Suggests	crlmm(>= 1.17.14), RUnit
SystemRequirements
Enhances	doSNOW, VanillaICE(>= 1.21.24), RColorBrewer
URL	http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
Depends On Me	mBPCR
Imports Me	crlmm, phenoTest
Suggests Me	MinimumDistance, oligoClasses, VanillaICE
Links To Me
Build Report

Package Archives

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

Source Package	SNPchip_2.32.0.tar.gz
Windows Binary	SNPchip_2.32.0.zip
Mac OS X 10.11 (El Capitan)	SNPchip_2.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SNPchip
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SNPchip
Package Short Url	https://bioconductor.org/packages/SNPchip/
Package Downloads Report	Download Stats