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>

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

Installation

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


if (!require("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")
Plotting Idiograms PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, GeneticVariability, SNP, Software, Visualization
Version 2.32.0
In Bioconductor since BioC 2.0 (R-2.5) (17 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)
System Requirements
URL http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
See More
Suggests crlmm(>= 1.17.14), RUnit
Linking To
Enhances doSNOW, VanillaICE(>= 1.21.24), RColorBrewer
Depends On Me mBPCR
Imports Me crlmm, phenoTest
Suggests Me MinimumDistance, oligoClasses, VanillaICE
Links To Me
Build Report 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
Old Source Packages for BioC 3.10 Source Archive