SNPchip

Classes and Methods for high throughput SNP chip data

Bioconductor version: 2.5

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 <rscharpf at jhsph.edu> and Ingo Ruczinski

Maintainer: Robert Scharpf <rscharpf at jhsph.edu>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("SNPchip")

Documentation

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

Details

biocViews	CopyNumberVariants, SNP, GeneticVariability, Visualization
Depends	R (>= 2.6.0), Biobase(>= 2.5.5), methods, oligoClasses(>= 1.7.8), graphics
Imports	Biobase(>= 2.5.5), graphics, grDevices, methods, oligoClasses(>= 1.7.8), 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	crlmm, VanillaICE
Suggests Me	Category
Version	1.10.0
Since	Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source	SNPchip_1.10.0.tar.gz
Windows Binary	SNPchip_1.10.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	SNPchip_1.10.0.tgz
Package Downloads Report	Download Stats

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