SNPchip

Classes and Methods for high throughput SNP chip data

Bioconductor version: Development (2.8)

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:///biocLite.R")
biocLite("SNPchip")    

Documentation

PDF R Script SNPchip Vignette

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
Version 1.15.1

Package Downloads

Package Source SNPchip_1.15.1.tar.gz
Windows Binary SNPchip_1.15.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary SNPchip_1.15.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center