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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPchip")
In most cases, you don't need to download the package archive at all.
SNPchip
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see 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>
Citation (from within R,
enter citation("SNPchip")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPchip")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SNPchip")
| SNPchip.pdf | ||
| Reference Manual |
Details
| biocViews | CopyNumberVariants, GeneticVariability, SNP, Software, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (9 years) |
| License | LGPL (>= 2) |
| 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 |
| LinkingTo | |
| Suggests | RSQLite, VanillaICE, RColorBrewer, genefilter, pd.mapping50k.xba240 |
| SystemRequirements | |
| Enhances | |
| URL | http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html |
| Depends On Me | mBPCR |
| Imports Me | crlmm, VanillaICE |
| Suggests Me | Category |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SNPchip_1.16.0.tar.gz |
| Windows Binary | SNPchip_1.16.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SNPchip/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/SNPchip/ |
| Package Downloads Report | Download Stats |
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