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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("genoset")
In most cases, you don't need to download the package archive at all.
genoset
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see genoset.
Provides classes similar to ExpressionSet for copy number analysis
Bioconductor version: 3.0
Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a GRanges object. This object contains feature genome location data and provides for efficient subsetting on genome location. Provides convenience functions for processing of copy number and B-Allele Frequency data. Provides the class RleDataFrame to store runs of data along the genome for multiple samples.
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")
| R Script | genoset | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, DataRepresentation, Infrastructure, Microarray, SNP, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), BiocGenerics(>= 0.11.3), Biobase(>= 2.15.1), GenomicRanges(>= 1.17.19) |
| Imports | S4Vectors(>= 0.2.3), GenomeInfoDb(>= 1.1.3), IRanges, methods, graphics |
| LinkingTo | |
| Suggests | RUnit, DNAcopy, stats, BSgenome, Biostrings |
| SystemRequirements | |
| Enhances | parallel |
| URL | https://github.com/phaverty/genoset |
| Depends On Me | VegaMC |
| Imports Me | methyAnalysis |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | genoset_1.20.0.tar.gz |
| Windows Binary | genoset_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | genoset_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | genoset_1.20.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/genoset/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/genoset/ |
| Package Downloads Report | Download Stats |
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