- Home
- Bioconductor 2.10
- Software Packages
- genoset
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genoset")
In most cases, you don't need to download the package archive at all.
genoset
|
This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see genoset.
Provides classes similar to ExpressionSet for copy number analysis
Bioconductor version: 2.10
Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a RangedData object from the IRanges package. This object contains feature genome location data and provides for simple subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.
Author: Peter M. Haverty
Maintainer: Peter M. Haverty <phaverty at gene.com>
Citation (from within R,
enter citation("genoset")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genoset")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("genoset")
| genoset | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariants, DataRepresentation, Infrastructure, Microarray, SNP, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods, BiocGenerics(>= 0.1.6), Biobase(>= 2.15.1), IRanges(>= 1.13.5), bigmemory, GenomicRanges |
| Imports | methods, BiocGenerics, Biobase, DNAcopy, graphics, IRanges, stats, GenomicRanges, Biostrings, BSgenome, bigmemory |
| LinkingTo | |
| Suggests | RUnit |
| SystemRequirements | |
| Enhances | parallel, BSgenome.Hsapiens.UCSC.hg19 |
| URL | |
| Depends On Me | VegaMC |
| Imports Me | lumi |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | genoset_1.6.0.tar.gz |
| Windows Binary | genoset_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/genoset/tree/release-2.10 |
| Package Short Url | http://bioconductor.org/packages/genoset/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
