To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cpvSNP")
In most cases, you don't need to download the package archive at all.
cpvSNP
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see cpvSNP.
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Bioconductor version: 3.3
Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.
Author: Caitlin McHugh, Jessica Larson, and Jason Hackney
Maintainer: Caitlin McHugh <mchughc at uw.edu>
Citation (from within R,
enter citation("cpvSNP")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cpvSNP")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cpvSNP")
| R Script | Running gene set analyses with the "cpvSNP" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), GenomicFeatures, GSEABase(>= 1.24.0) |
| Imports | methods, corpcor, BiocParallel, ggplot2, plyr |
| LinkingTo | |
| Suggests | TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cpvSNP_1.4.0.tar.gz |
| Windows Binary | cpvSNP_1.4.0.zip |
| Mac OS X 10.9 (Mavericks) | cpvSNP_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/cpvSNP/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/cpvSNP/ |
| 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
