SNPchip

Classes and Methods for high throughput SNP chip data

This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing.

Author	Robert Scharpf and Ingo Ruczinski
Maintainer	Robert Scharpf

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("SNPchip")

Documentation

SNPchip Vignette	PDF	R Script
oligoHowTo Vignette	PDF	R Script
Reference Manual

Details

biocViews	CopyNumberVariants , SNP , GeneticVariability , Visualization
Depends	R , Biobase , methods , oligoClasses , graphics
Imports	Biobase , graphics , grDevices , methods , oligoClasses , stats , utils
Suggests	RSQLite , VanillaICE , RColorBrewer , genefilter , pd.mapping50k.xba240
System Requirements
License	LGPL (>= 2)
URL	http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
Depends On Me	mBPCR
Imports Me	VanillaICE , crlmm
Suggests Me	Category

Package Downloads

Package source	SNPchip_1.10.0.tar.gz
Windows binary	SNPchip_1.10.0.zip
MacOS X 10.4 (Tiger) binary	SNPchip_1.10.0.tgz
MacOS X 10.5 (Leopard) binary	SNPchip_1.10.0.tgz
Package Downloads Report	Downloads Stats