SNPchip

Classes and Methods for high throughput SNP chip data

Bioconductor version: 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 <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 SNPchip Vignette
PDF   Reference Manual

Details

biocViews CopyNumberVariants, SNP, GeneticVariability, Visualization
Depends R (>= 2.10.0), Biobase(>= 2.7.4), methods, oligoClasses(>= 1.9.52), graphics
Imports Biobase(>= 2.7.4), graphics, grDevices, methods, oligoClasses(>= 1.9.52), 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 1.16.0
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source SNPchip_1.16.0.tar.gz
Windows Binary SNPchip_1.16.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary SNPchip_1.16.0.tgz
Package Downloads Report Download Stats

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